Having trouble restoring files removed by MalwareBytes

Okay, so here's the deal. I went out of town for awhile and let my roommates use my computer. When I got back, there was a bunch of Malware on my computer. After doing a little searching, I found MalwareBytes. So after I downloaded and ran it, it detected and removed a large amount of files. So after restarting, I noticed that half my desktop programs were missing their icons. When I got on the internet to try and resolve the problem, my browser was running really slow. So I reinstalled Chrome (it was at this point that my browsing history was removed, so I don't have a way of figuring out where I downloaded MalwareBytes from), and it was still running really slow. After that I really didn't do much to try and resolve the problem. That was over a month ago, and now I just recently realized that there are a few more serious problems that were caused by that. When I tried to open one of the programs that were missing icons, nothing happened. That is when I realized that the files that MWB thought were threats, were in fact a seriously large amount of my system files and program files. I am missing a 25GB game, Skype, Wise Registry Cleaner, Tux Guitar, Daemon Tools Lite, AVG, even MalwareBytes itself. Who knows what else I am missing that I don't know of yet. The thing is, my hard drive does not indicate that I have freed up any space since then. So are the files still somewhere on my computer? If they are then they are hidden pretty well. Because I have checked Compatibility Files, and almost every folder on the disk. I even set my computer to show hidden files and folders. Still, to no avail. All my system restore points have also been removed by MWB. And since it has been more than a month since this has all happened, I don't know if I can use a restore program to get the files back. Am I totally screwed? I can't find anything on the net that can help me.

Edit: Turns out the shortcuts were just edited to point directly to the desktop, instead of their target files. I was looking in the wrong folder for the game. The game is called Star Wars the Old Republic, and I was looking in the nearly empty folder of Star Wars KNIGHTS of the Old Republic. So for now, as annoying as it may be, it seems the only thing wrong is my shortcuts and the fact that I now have no system restore points.

Hello and welcome progfrog mate for starters I would not have any rubbish ware like AVG Wise registry cleaner Daemon tools on any of my machines but it is your choice of course.

Now if you run this it might get back a fair bit of what you have lost - or not but certainly worth a try
https://www.piriform.com/recuva/download see what you can get back.

Now I would also make yourself the admin account owner to stop your roommates from making any major program or machines changes too.

Ok mate try these too
SFC /SCANNOW Command - System File Checker
Disk Check < if necessary include the /f and /r in the command line as per Option2

If you are interested too this is good - my bible and point 9 is a good place to start I untick all start up items
Optimize Windows 7