Well, if you want to start fresh and remove all hacks, I'd re-install vB by uploading all your files from a fresh copy. From there, mod and hack your site as you see fit.
I had to do this with one of my installs. I had so many problems, I just decided to start from scratch.
One tip that will help you in the future. Use comment tags for everything that you do, so that you can always tell what belongs there and what was added. You can NEVER have enough comment tags.