Suite Upgrading from 3.8.4 - A little differently, though
 

This weekend, I plan to upgrade the forum software of the site I work for, but there's a catch: At some point in time (about two months ago), the files for our current version of vBulletin 3.8.4 got all screwed up. I won't go into any theories about how/why/etc. Every file failed a verification check, and to fix it, I had to copy over all the old files with a fresh copy of 3.8.4 files. That fixed the forum about 90% of way.

Since then, we've had some odd issues, and no resolutions. We're upgrading to 4.0 to not only hopefully resolve our current issues, but also to leverage the new features specifically available in the SUITE. Here is my question:

Just to make sure that the issues we're experiencing now don't even remotely get carried over, will I be able to just delete all 3.8.4 files (keeping the database as is, of course), and uploading the new 4.0 files and perform an update at that point, or will that screw things up? Are there files from 3.8.4 that the upgrade script for 4.0 look for while doing the upgrade? I want to delete all files pertaining to 3.8.4 because I don't even want to risk bringing over any problems we're currently having. If problems are present after our upgrade, I want to be able to eliminate any pre-existing issues as a possible culprit.

I hope my questions makes sense. Any help that you can provide would be greatly appreciated. Thanks so much.