Sorry for not responding... work is keeping me busy.
Anyway, when I go Manage Applications, select Filter~>All and go down to Market there is nothing to do with Uninstall. I tried long clicking and that did nothing. When I click on Market, the only buttons are Clear Cache, Clear Defaults, and Force Stop. Am I missing something?
To answer other questions, both the JI6 and JFD .tar files I used (found on xda) came with their own .pit files and I did use the respective .pit files when flashing. After the flash, all I do is install Appbrain and start loading my applications again (no other restoration methods). I've run fix_permissions and that didn't help when I ran it though I've only done it once or twice in the whole process.
Note - I have Market 1714.