The site is now clean, vBulletin files have been upgraded and some security plugins were installed. I've submitted a request to Google so that we aren't flagged anymore. Should take a few days at most. I'm looking into CloudFlare and other security buffs as well.
I'm also speaking with another person regarding the technical issues of the site. Which include, but are not limited to, being unable to quote, being unable to edit posts, certain tags not working, search not working and so on. He should be deploying a test server soon so that he can come up with a solution to implement on the site itself.
"Don't count the days, make the days count"