I would imagine along the lines of what @retroroscoe mentioned, 10.11 is less an issue than Server.app v5. There have been a few discussions around some of the problems it causes, and JAMF actually as a defect number for how Server.app v5 and its port reservations keep the JDS from working.
I held off a few weeks but I finally decided to go ahead with the upgrade.
Ok, so the two things that have been causing issues is server 5 where it takes port 8443, which had automatically installed through auto updates... which can be fixed by commenting out port 8443 by running
sudo nano /Library/Server/Web/Config/Proxy/apache_serviceproxy.conf
Then when I upgraded, I unfortunately upgraded to 10.11 and then upgraded to 10.11.1 instead of installing 10.11.1
the install process, wether it was the jump from 10.11 to 10.11.1 killed apache, well technically the java idk 7 was not functioning.
To fix this I had to backup sql, which I had done prior to the upgrade, but also backed up jss folder, and then run the 9.81 jss install again, which instructed me to get the latest JRE and JDK builds, and the Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files 8 Download
as the jss install instructed...
The install took a lot long retain previously, but as a result everything came back fine.
I also had issues with paper cut, we have virtual printers set on our mac server, I had to remove their listings and rebuild them, then afterwards running the Control Printer Monitoring.command
I then had to rebuild their virtual printer features in paper cut.
After doing so that came good also.
Apple config v1.7 is playing up, so I am still deciding on wether to stay on this os version, I am not really interested in moving to v2 just yet.