So i was having simliar issues with re-direct (and then subsequent failures with no re-direct in place)
My problem was eventually solved by modifying the acme_tiny.py to behave itself and disable a check, my full thread is here: https://community.letsencrypt.org/t/virtualmin-lets-encrypt-web-based-validation-failed/
However, the snippiets of information i suspect might help you (if you dont want to remove global redirects). Here was my .htaccess file with a redirect exception for the .well-known folder struture. Give it a try.
RewriteEngine On
RewriteRule ^.well-known/acme-challenge/ - [L]
RewriteCond %{HTTPS} !=on
RewriteRule ^/?(.*) https://%{HTTP_HOST}/$1 [R,L]
One thing mentioned to me also was that the Let’s encrypt script runs in memory, i was restarting apache, but i ended up just restarting my host to make 100% sure it wasnt anything within memory.
Depending on how that goes, and if you stop getting DNS failures, you might need to disable a check
add disable_check=True at line 139. Add it below the comment “# check that the file is in place”, but above “try:
wellknown_url = “http://{0}/.well-known/acme-challenge/{1}”.format(domain, token)”
blah blah.
Otherwise take a look at the first response in this post to try and resolve some of the other underlying issues your site has.
Also, you listed your webmin version in the above post (1.941), rather than your actual virutalmin version. Might be worth an edit to correct that so others can see.
For example, mine: 