I have a few custom templates that I use for Gallery. I upgraded to 1.0.1 from RC3 today and for some reason the new templates didn't override the existing ones. I don't mind if my custom ones are lost since most of them were features that are not included.
Using the install file to install the templates also does nothing since I'm assuming it doesn't overwrite. How would I go about removing my existing templates so I could install the new ones without doing a full reinstall?
You need to revert any templates that you have modified. That's the way vBulletin's templating system works. Even when you do a vBulletin upgrade, it doesn't update any templates that you have modified.