Special Intermediate Steps to Upgrade From VBSEO 3.1.0

I just tried to upgrade my vbseo from 3.1.0 to the current 3.6.0 RC2, and when I did, carefully overwriting folders and files, no pages deeper than the main index page would appear, including anything within the admincp (making it hard to make any adjustments).

Thankfully I backed everything up beforehand and just overwrote the new files with the old and everything is fine again.

However, I noticed there are a few files that didn't get overwritten with the new version, and folders and files that are new to this version that weren't around in 3.1.0.

So. Are there interim steps I need to take before I can make this upgrade? Or do I need to upgrade my version of vBulletin first?

Thanks in advance.

Should I completely uninstall and reinstall?

I'm bleeding traffic like a knife wound right now because every Google search result is appended to include a warning that the site may harm your computer. So I'd like to get this fixed as soon as I can.

replied to your ticket.