Ben,
1.) I just followed the instructions to fix the themes link and that worked great.
2.) I didn't know by adding .5 after an value in an order box would renumber everything after that value. The little things in life...
3.) I executed the query and ran the module again and no errors came up.
4.) I installed the audit module. I'll keep an eye on it and see if anything comes up in regards to permissions being changed.
Thanks for all your help.
Update: I just checked out the audit log, and all the permissions were updated at 1:54 PM for every single user.
1.) I just followed the instructions to fix the themes link and that worked great.
2.) I didn't know by adding .5 after an value in an order box would renumber everything after that value. The little things in life...

3.) I executed the query and ran the module again and no errors came up.
4.) I installed the audit module. I'll keep an eye on it and see if anything comes up in regards to permissions being changed.
Thanks for all your help.
Update: I just checked out the audit log, and all the permissions were updated at 1:54 PM for every single user.