Complete defragmentation isn't necessary and the stock defrag program doesn't do a complete defrag. Doing a complete defrag isn't useful.
Say you got a 1 GB video file that's in 3 pieces. That doesn't matter because the seeking to the fragmented sector will be faster than the buffer runs out of data. If you defrag that, you're just wasting a lot of time.
It's small files that need defrag. The buffer runs out before the fragmented seek. That's why the stock defrag takes an hour. It doesn't move big data. And that's ok, because it doesn't matter.
A drive can be very fragmented and still function if slowly. The program you want to be running is chkdsk.
You should take it easy on aftermarket utilities. They can often cause more trouble than they cure. That's especially since a lot of these file utilities were written for other versions of windows. You can really fry stuff if you don't watch it.
I think you are more likely to fix issues with regular windows utilities. If you load up some other program for something windows can already do, you should have an extremely good reason.
Running an aftermarket defrag program? I wouldn't. The possibility of running into Trojans, virus, or it just plain screwing your system up are too high.
Right now, I'd run chkdsk. Make sure you turn the fix option on. Then I'd proceed to looking at system restore points. Then I'd try the "upgrade" method of system cleanup I linked above. If that didn't work... I'd just wipe and start over.
You should be done by lunch.
The more you monkey around with this, the less likely you're gonna get a happy outcome.
Make sure you look at S.M.A.R.T. in detail for anything that looks suspicious. Look for incidents of the drive overheating. Is the temperature ok? You shouldn't be getting much more that 50 C. 45 would be more normal. If that isn't ok? Are you dirty? Do you have a fan out? Hot is a sign of worn out too... so that's something to consider.
If it's a Western Digital drive, you might take SUPER high temperatures with a grain of salt. WD drives are known for fritzy thermal sensors. Put your finger on the drive. If that's uncomfortable, it's too hot.