hi @csilver
I did :D, apologies for the delays I misread your message and would have sent something through sooner 
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I believe the root cause is the bindings that config.bat creates are inaccurate so I used the instructions here instead: Running JIRA applications over SSL or HTTPS | Administering Jira applications Data Center and Server 7.3 | Atlassian Documentation - the advanced section
I had a JKS I created in this tutorial Tutorial - Java KeyStores (JKS) With Let's Encrypt - #7 by ahaw021. As long as your JKS is in line (use the KeyExplorer tool to confirm) you should have no issues
Server.xml file updated manually
<Connector port="8443" protocol="org.apache.coyote.http11.Http11NioProtocol" maxHttpHeaderSize="8192" SSLEnabled="true" maxThreads="150" minSpareThreads="25" enableLookups="false" disableUploadTimeout="true" acceptCount="100" scheme="https" secure="true" sslEnabledProtocol="TLSv1.2" clientAuth="false" sslProtocol="TLSv1.2" useBodyEncodingForURI="true" keyAlias="simple-cert" keystoreFile="D:\LETSENCRYPT\JAVA-KEY-TOOL\letsencrypt.jks" keystorePass="test12345" keystoreType="JKS"/>
Running Using localhost:8443 (errors occur due to name matching but right cert is used)
Running using jks-simple-cert.firecube.xyz pointing to localhost
Note: this is a bit of hack don't use it in production. Setup proper DNS.
Andrei