Dear Casey,
No worries and thank you for the information, really useful as I can see what is what. You do appear to have a long list of extras .
The DB changes would not have caused the issue rather that the underlying core code changes that the plugin's rely on. I think the next step for you if things are not working is to remove all of the add-ons and switch to a standard theme temporarily then put them back one by one. In that way you can test and discover which plugin is causing the issue. Just like the 'course-menu' as you discovered. Unfortunately I've found that PHP can be more work / no work with not so much middle ground upon which to recover.
Indeed I could not find a course-menu version for 2.3 or in fact 'games'.
When you say 'Course topic - no longer shows in a format that collapses' what do you mean as the standard topics format does not collapse?
Cheers,
Gareth