After some tinkering yesterday I had gotten all of my issues to go away by

Copying all files from the Titanium Everquest folder that you should have backed up before upgrading.
Copy them into new UF folder.
When given the option to copy over existing files, select "do this for next X amount of conflicts" and then select "dont copy / no"

Profit.

I've exhausted my abilities with a search function and I was unable to come up with anything. Recently I switched to UF client and after logging in everything was visible aside from the Shadowknight epic 3.0 and 3.5. In-game, I was told there was a fix out there but I was unable to find it. Could someone please point me in the right direction? Thanks