There are a couple possible problems here. I'm not sure which one is your problem, so I'll describe both and you can choose your own adventure. ;-)
Option 1: Your hard drive is failing...
This would manifest itself in a few hard-to-detect ways (various files going bad) and eventually, it would result in a vital system file getting corrupted. That would explain why you were missing some system32 files (in my experience, missing system files are the first un-ignorable sign of a failing hard drive).
Even though you repaired the system files, you didn't fix the failing hard drive. You are continuing to experience issues related to your failing hard drive and that is why your computer is slow.
Option 2: You have excessive cruddy software
If you have a lot of bad software (either malicious, poorly written, or both) on your computer, it might have eventually conspired in such a way to corrupt some system files and result in your missing system32 files problems. Then, since you did a repair install (instead of a full reinstall), it just ignored those cruddy programs, but now they're missing some components that got wiped out during the repair process. The errors caused by those missing components could result in the slow performance you're seeing now.
Option 3: A combination of options 1 and 2
Of course, while I would bet on option 1, it's quite likely that your problems are a result of both a bad hard drive AND bad software. Of course, the solution to options 1 and 3 are the same: get a new hard drive. And the solution to option 2 is to reformat the drive you have.
Since you probably don't want to lose your data, I'm going to go ahead and recommend you just buy a new hard drive. You can keep the old hard drive attached as a secondary internal drive (or as an external drive if you have a laptop). Just get a new drive, put it in, install Windows on it, and then plug in the old drive to rescue your important data. If the old drive really is going bad, you should get rid of it and not store anything important on it. But that's up to you. Don't say I didn't warn you.
A replacement drive shouldn't cost more than about $75 unless you're looking at something high-capacity (like a 500GB laptop drive or a 1TB+ desktop drive). You should be able to do the handiwork yourself. So it should be a pretty easy and cheap fix (as computer fixes go).
Good luck!