Switching from DNS to Webroot results in Apache unable to start

I had created those other virtual hosts because I was thinking each separate certificate needed it's own location

This looks correct:

[ I don't know why it doesn't show in the output - one more Apache weirdness ]

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So... does Apache now start?

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issuing: sudo systemctl start apache2

See "systemctl status apache2.service" and "journalctl -xe" for details.

systemctl status apache2.service shows:

* apache2.service - The Apache HTTP Server
     Loaded: loaded (/lib/systemd/system/apache2.service; enabled; vendor preset: enabled)
     Active: failed (Result: exit-code) since Tue 2021-12-28 12:22:29 PST; 1min 13s ago
       Docs: https://httpd.apache.org/docs/2.4/
    Process: 666734 ExecStart=/usr/sbin/apachectl start (code=exited, status=1/FAILURE)

Dec 28 12:22:29 fungi systemd[1]: Starting The Apache HTTP Server...
Dec 28 12:22:29 fungi apachectl[666742]: [Tue Dec 28 12:22:29.728221 2021] [alias:warn] [pid 666742:tid 140581958831168] AH00671: The Alias directive in /etc/apache2/apache2.conf at line 231 will probably never match because it overlaps an earlier Alias.
Dec 28 12:22:29 fungi apachectl[666734]: Action 'start' failed.
Dec 28 12:22:29 fungi apachectl[666734]: The Apache error log may have more information.
Dec 28 12:22:29 fungi systemd[1]: apache2.service: Control process exited, code=exited, status=1/FAILURE
Dec 28 12:22:29 fungi systemd[1]: apache2.service: Failed with result 'exit-code'.
Dec 28 12:22:29 fungi systemd[1]: Failed to start The Apache HTTP Server.

sudo apache2 --help shows

[Tue Dec 28 13:39:22.512932 2021] [core:warn] [pid 667219] AH00111: Config variable ${APACHE_RUN_DIR} is not defined
apache2: Syntax error on line 80 of /etc/apache2/apache2.conf: DefaultRuntimeDir must be a valid directory, absolute or relative to ServerRoot

line 80 of /etc/apache2/apache2.conf is

DefaultRuntimeDir ${APACHE_RUN_DIR}

On this page server - Ubuntu Apache2 DefaultRuntimeDir must be a valid directory, absolute or relative to ServerRoot - Ask Ubuntu it says I need to change the DocumentRoot in /etc/apache2/sites-enabled/000-default.conf but my system doesn't have that file. My system does have a default-ssl.conf in that directory. It says to change the DocumentRoot in that file. I changed mine to DocumentRoot /var/www/66tr.ee That did not work. Then I tried DocumentRoot /var/www still getting the same 'exit-code' from systemd.

Let's have a look at this file:

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sudo tail -n 2 /var/log/apache2/error.log is showing:

[Tue Dec 28 15:12:55.098339 2021] [ssl:emerg] [pid 667943:tid 140529194245184] AH02311: Fatal error initialising mod_ssl, exiting. See /var/log/apache2/error.log for more information
AH00016: Configuration Failed

/etc/apache2/apache2.conf:

# This is the main Apache server configuration file.  It contains the
# configuration directives that give the server its instructions.
# See http://httpd.apache.org/docs/2.4/ for detailed information about
# the directives and /usr/share/doc/apache2/README.Debian about Debian specific
# hints.
#
#
# Summary of how the Apache 2 configuration works in Debian:
# The Apache 2 web server configuration in Debian is quite different to
# upstream's suggested way to configure the web server. This is because Debian's
# default Apache2 installation attempts to make adding and removing modules,
# virtual hosts, and extra configuration directives as flexible as possible, in
# order to make automating the changes and administering the server as easy as
# possible.

# It is split into several files forming the configuration hierarchy outlined
# below, all located in the /etc/apache2/ directory:
#
#	/etc/apache2/
#	|-- apache2.conf
#	|	`--  ports.conf
#	|-- mods-enabled
#	|	|-- *.load
#	|	`-- *.conf
#	|-- conf-enabled
#	|	`-- *.conf
# 	`-- sites-enabled
#	 	`-- *.conf
#
#
# * apache2.conf is the main configuration file (this file). It puts the pieces
#   together by including all remaining configuration files when starting up the
#   web server.
#
# * ports.conf is always included from the main configuration file. It is
#   supposed to determine listening ports for incoming connections which can be
#   customized anytime.
#
# * Configuration files in the mods-enabled/, conf-enabled/ and sites-enabled/
#   directories contain particular configuration snippets which manage modules,
#   global configuration fragments, or virtual host configurations,
#   respectively.
#
#   They are activated by symlinking available configuration files from their
#   respective *-available/ counterparts. These should be managed by using our
#   helpers a2enmod/a2dismod, a2ensite/a2dissite and a2enconf/a2disconf. See
#   their respective man pages for detailed information.
#
# * The binary is called apache2. Due to the use of environment variables, in
#   the default configuration, apache2 needs to be started/stopped with
#   /etc/init.d/apache2 or apache2ctl. Calling /usr/bin/apache2 directly will not
#   work with the default configuration.


# Global configuration
#

#
# ServerRoot: The top of the directory tree under which the server's
# configuration, error, and log files are kept.
#
# NOTE!  If you intend to place this on an NFS (or otherwise network)
# mounted filesystem then please read the Mutex documentation (available
# at <URL:http://httpd.apache.org/docs/2.4/mod/core.html#mutex>);
# you will save yourself a lot of trouble.
#
# Do NOT add a slash at the end of the directory path.
#
#ServerRoot "/etc/apache2"

#
# The accept serialization lock file MUST BE STORED ON A LOCAL DISK.
#
#Mutex file:${APACHE_LOCK_DIR} default

#
# The directory where shm and other runtime files will be stored.
#

DefaultRuntimeDir ${APACHE_RUN_DIR}

#
# PidFile: The file in which the server should record its process
# identification number when it starts.
# This needs to be set in /etc/apache2/envvars
#
PidFile ${APACHE_PID_FILE}

#
# Timeout: The number of seconds before receives and sends time out.
#
Timeout 300

#
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to "Off" to deactivate.
#
KeepAlive On

#
# MaxKeepAliveRequests: The maximum number of requests to allow
# during a persistent connection. Set to 0 to allow an unlimited amount.
# We recommend you leave this number high, for maximum performance.
#
MaxKeepAliveRequests 100

#
# KeepAliveTimeout: Number of seconds to wait for the next request from the
# same client on the same connection.
#
KeepAliveTimeout 5


# These need to be set in /etc/apache2/envvars
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}

#
# HostnameLookups: Log the names of clients or just their IP addresses
# e.g., www.apache.org (on) or 204.62.129.132 (off).
# The default is off because it'd be overall better for the net if people
# had to knowingly turn this feature on, since enabling it means that
# each client request will result in AT LEAST one lookup request to the
# nameserver.
#
HostnameLookups Off

# ErrorLog: The location of the error log file.
# If you do not specify an ErrorLog directive within a <VirtualHost>
# container, error messages relating to that virtual host will be
# logged here.  If you *do* define an error logfile for a <VirtualHost>
# container, that host's errors will be logged there and not here.
#
ErrorLog ${APACHE_LOG_DIR}/error.log

#
# LogLevel: Control the severity of messages logged to the error_log.
# Available values: trace8, ..., trace1, debug, info, notice, warn,
# error, crit, alert, emerg.
# It is also possible to configure the log level for particular modules, e.g.
# "LogLevel info ssl:warn"
#
LogLevel warn

# Include module configuration:
IncludeOptional mods-enabled/*.load
IncludeOptional mods-enabled/*.conf

# Include list of ports to listen on
Include ports.conf


# Sets the default security model of the Apache2 HTTPD server. It does
# not allow access to the root filesystem outside of /usr/share and /var/www.
# The former is used by web applications packaged in Debian,
# the latter may be used for local directories served by the web server. If
# your system is serving content from a sub-directory in /srv you must allow
# access here, or in any related virtual host.
<Directory />
	Options FollowSymLinks
	AllowOverride None
	Require all denied
</Directory>

<Directory /usr/share>
	AllowOverride None
	Require all granted
</Directory>

<Directory /var/www/>
	Options Indexes FollowSymLinks
	AllowOverride None
	Require all granted
</Directory>

#<Directory /srv/>
#	Options Indexes FollowSymLinks
#	AllowOverride None
#	Require all granted
#</Directory>

ServerName fungi.66tr.ee
#ServerName localhost

# AccessFileName: The name of the file to look for in each directory
# for additional configuration directives.  See also the AllowOverride
# directive.
#
AccessFileName .htaccess

#
# The following lines prevent .htaccess and .htpasswd files from being
# viewed by Web clients.
#
<FilesMatch "^\.ht">
	Require all denied
</FilesMatch>


#
# The following directives define some format nicknames for use with
# a CustomLog directive.
#
# These deviate from the Common Log Format definitions in that they use %O
# (the actual bytes sent including headers) instead of %b (the size of the
# requested file), because the latter makes it impossible to detect partial
# requests.
#
# Note that the use of %{X-Forwarded-For}i instead of %h is not recommended.
# Use mod_remoteip instead.
#
LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined
LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %O" common
LogFormat "%{Referer}i -> %U" referer
LogFormat "%{User-agent}i" agent

# Include of directories ignores editors' and dpkg's backup files,
# see README.Debian for details.

# Include generic snippets of statements
IncludeOptional conf-enabled/*.conf

# Include the virtual host configurations:
IncludeOptional sites-enabled/*.conf

ServerTokens Prod
ServerSignature Off 

# from 100-letsencrypt.conf
Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/

# Bypass Auth
<IfModule mod_access_compat.c>
  <Directory /var/www/letsencrypt/.well-known/acme-challenge/>
    Satisfy any
  </Directory>
</IfModule>

# Redirect before other rewrite rules
RewriteCond %{REQUEST_URI} /\.well\-known/acme\-challenge/
RewriteRule (.*) /.well-known/acme-challenge/$1 [L,QSA]

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

The conflict seems to be coming from an included file.
Please show:
sudo grep -iR alias /etc/apache2/

Also, setting the ServerName to anything you might want to use later isn't a good idea:
ServerName fungi.66tr.ee

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sudo grep -iR alias /etc/apache2/:

/etc/apache2/sites-enabled/66tr.ee.conf:	ServerAlias www.66tr.ee
/etc/apache2/sites-enabled/66tr.ee.conf:        ServerAlias www.66tr.ee
/etc/apache2/conf-available/letsencrypt.conf:Alias /.well-known/acme-challenge/ "/var/lib/letsencrypt/.well-known/acme-challenge/"
/etc/apache2/conf-available/serve-cgi-bin.conf:<IfModule mod_alias.c>
/etc/apache2/conf-available/serve-cgi-bin.conf:		ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
/etc/apache2/conf-available/localized-error-pages.conf:# We use Alias to redirect any /error/HTTP_<error>.html.var response to
/etc/apache2/conf-available/localized-error-pages.conf:#Alias /error/include/ "/your/include/path/"
/etc/apache2/conf-available/localized-error-pages.conf:# even on a per-VirtualHost basis.  If you include the Alias in the global server
/etc/apache2/conf-available/localized-error-pages.conf:# context, is has to come _before_ the 'Alias /error/ ...' line.
/etc/apache2/conf-available/localized-error-pages.conf:# The internationalized error documents require mod_alias, mod_include
/etc/apache2/conf-available/localized-error-pages.conf:#		<IfModule mod_alias.c>
/etc/apache2/conf-available/localized-error-pages.conf:#			Alias /error/ "/usr/share/apache2/error/"
/etc/apache2/sites-available/localhost.conf:  Alias "/config.js" "/etc/jitsi/meet/localhost-config.js"
/etc/apache2/sites-available/localhost.conf:  Alias "/external_api.js" "/usr/share/jitsi-meet/libs/external_api.min.js"
/etc/apache2/sites-available/100-letsencrypt.conf:Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/
/etc/apache2/sites-available/66tr.ee.conf:	ServerAlias www.66tr.ee
/etc/apache2/sites-available/66tr.ee.conf:        ServerAlias www.66tr.ee
/etc/apache2/mods-available/mime.conf:	# To use CGI scripts outside of ScriptAliased directories:
/etc/apache2/mods-available/proxy_balancer.load:# Depends: proxy alias slotmem_shm
/etc/apache2/mods-available/alias.conf:<IfModule alias_module>
/etc/apache2/mods-available/alias.conf:	# Aliases: Add here as many aliases as you need (with no limit). The format is
/etc/apache2/mods-available/alias.conf:	# Alias fakename realname
/etc/apache2/mods-available/alias.conf:	# require it to be present in the URL.  So "/icons" isn't aliased in this
/etc/apache2/mods-available/alias.conf:	# We include the /icons/ alias for FancyIndexed directory listings.  If
/etc/apache2/mods-available/alias.conf:	# Alias line below was commented
/etc/apache2/mods-available/alias.conf:	#Alias /icons/ "/var/www/html/VicsPlace/icons"
/etc/apache2/mods-available/alias.load:LoadModule alias_module /usr/lib/apache2/modules/mod_alias.so
/etc/apache2/mods-available/vhost_alias.load:LoadModule vhost_alias_module /usr/lib/apache2/modules/mod_vhost_alias.so
/etc/apache2/mods-enabled/mime.conf:	# To use CGI scripts outside of ScriptAliased directories:
/etc/apache2/mods-enabled/alias.conf:<IfModule alias_module>
/etc/apache2/mods-enabled/alias.conf:	# Aliases: Add here as many aliases as you need (with no limit). The format is
/etc/apache2/mods-enabled/alias.conf:	# Alias fakename realname
/etc/apache2/mods-enabled/alias.conf:	# require it to be present in the URL.  So "/icons" isn't aliased in this
/etc/apache2/mods-enabled/alias.conf:	# We include the /icons/ alias for FancyIndexed directory listings.  If
/etc/apache2/mods-enabled/alias.conf:	# Alias line below was commented
/etc/apache2/mods-enabled/alias.conf:	#Alias /icons/ "/var/www/html/VicsPlace/icons"
/etc/apache2/mods-enabled/alias.load:LoadModule alias_module /usr/lib/apache2/modules/mod_alias.so
/etc/apache2/apache2.conf:Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/
/etc/apache2/conf-enabled/letsencrypt.conf:Alias /.well-known/acme-challenge/ "/var/lib/letsencrypt/.well-known/acme-challenge/"
/etc/apache2/conf-enabled/serve-cgi-bin.conf:<IfModule mod_alias.c>
/etc/apache2/conf-enabled/serve-cgi-bin.conf:		ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
/etc/apache2/conf-enabled/localized-error-pages.conf:# We use Alias to redirect any /error/HTTP_<error>.html.var response to
/etc/apache2/conf-enabled/localized-error-pages.conf:#Alias /error/include/ "/your/include/path/"
/etc/apache2/conf-enabled/localized-error-pages.conf:# even on a per-VirtualHost basis.  If you include the Alias in the global server
/etc/apache2/conf-enabled/localized-error-pages.conf:# context, is has to come _before_ the 'Alias /error/ ...' line.
/etc/apache2/conf-enabled/localized-error-pages.conf:# The internationalized error documents require mod_alias, mod_include
/etc/apache2/conf-enabled/localized-error-pages.conf:#		<IfModule mod_alias.c>
/etc/apache2/conf-enabled/localized-error-pages.conf:#			Alias /error/ "/usr/share/apache2/error/"

Let's have a look at this file:
/etc/apache2/conf-enabled/letsencrypt.conf

sudo cat /etc/apache2/conf-enabled/letsencrypt.conf:

Alias /.well-known/acme-challenge/ "/var/lib/letsencrypt/.well-known/acme-challenge/"
<Directory "/var/lib/letsencrypt/">
    AllowOverride None
    Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
    Require method GET POST OPTIONS
</Directory>

Go ahead and delete all the duplicated lines (which are already included in the apache2.conf file).
[pretty much the entire file]

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Also, let's make sure this directory exists:
ls -l /var/www/letsencrypt/.well-known/acme-challenge/

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So delete everything that's already in /etc/apache2/sites-enabled/66tr.ee.conf from apache2.conf?

No.
Delete the file:

[whose content is already included in apache2.conf]

Although it is "spelled" differently:

"www" vs "lib"

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Deleted /etc/apache2/conf-enabled/letsencrypt.conf.
ls -l /var/www/letsencrypt/.well-known/acme-challenge/ outputs:
ls: cannot access '/var/www/letsencrypt/.well-known/acme-challenge/': No such file or directory

As I feared.
Do this:
mkdir -p /var/www/letsencrypt/.well-known/acme-challenge/

then again:
ls -l /var/www/letsencrypt/.well-known/acme-challenge/

then also:
sudo apachectl -t -D DUMP_VHOSTS

P.S. I hope you do realize that none of this has anything to do with this site.

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I realized it just before you came back on to help. I very much appreciate what you're doing. I kept thinking its going to lead back to the certbot command I first issued. I apologize

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