Reinstalling is not going to create extra categories
You sure you have ran any applicable upgrades if you upgraded?
You do not do any database scans AT ALL. You can run userfix.php if your totally sure your integration is fine.
However as I have said a few times if your xenforo importer changes usernames in any fashion you could have some ownership orphaning on photos or comments. Not too much I can do about that.
Aside from that if your integration is working then you should be working fine as far as that is concerned.