Thanks for the reply!
I'm not having any problems. I will deploy CAS to production in a few weeks and due some other infrastructure changes I'm forced (but happy) to do, I will need a new certificate. As I said, the Tomcat instances I have are already configured to be signed with CA certificates, and since Apache use them too, it means I only need to update those files to get it all working again.
I'm just lazy and due those 'mixed experiences' with jks containers I was curious if I could just use my certificates so CAS is signed as well once I get the new files. That being said, it just seems that I'll just need to spend some extra time and calmly work out the jks file, which is not really a bad thing.