Okay guys, I've been looking at a few files and I think I know which ones are corrupted. Luckily for me, I did take the priority of backing up before this incident occurred. I'm going to take off those ones that I believe are corrupted and put the back-ups on to there in the hopes that it will fix it.
If worse comes to worse, however, I may have to start over. This would be a serious thing, except for the fact that I have taken the liberty of backing up the .html files of my site. If it does come to worse, I'll be able to put them onto a new directory. A new directory though would mean a brand new site name.
So, if it does happen, I'll make sure to give it it's official .com/.net/.org name, and that will be it from then on out.
Hopefully, it won't have to come to that. -_-