Recent Graphical Lag

[vvilltaylor]

GPU: Zotac 970
CPU: i5 4690
OS: Windows 10
Using HDD
Fans for cooling system

I've recently been having issues with graphics processing.
I was able to run games like Fallout 4 at 60+ fps.
Warframe ran at above 100 fps or so.
I have however recently been getting 24-30 fps across the board.

What I have tried so far:

Checking GPU temp, pushes 55-58C
CPU temp keeps at about 45 per core

I have reinstalled graphics drivers

Attempted to clean up my files, got rid of large amounts that were unnecessary/unused (I used TuneUp Utilities 2014 for this).

Did a scan through TuneUp and found that my HDD is heavily fragmented, sitting at about 55gb heavy fragmentation, and I do believe I saw it to be about 120 gb of moderately fragmented (don't know how accurate these are).
Whenever I tried to finish the defrag through tuneup, it would get stuck at about 20%.
Tried rerunning it and it ended up getting stuck on 34% (been trying it since yesterday afternoon, left it on overnight and it got stuck).
Now I did have an issue with TuneUp in that it was opened in compatibility mode (due to me being on Windows 10), so I decided to look elsewhere for a defrag software.
The Windows application told me only about 4% was fragmented, but now I'm using Smart Defrag by IObit (as I saw it to be recommended elsewhere).
I ran the initial 'smart defrag' and it completed, but about 17% of my HDD was still fragmented.
I am running a more thorough run through, however it is puttering slowly and is also stuck on 20%.
It is going through the files rather slowly, but I'm going to try it for overnight.

Is there anything else that could be causing these problems?
I thought it was initially a driver update for Nvidia, but it seems to only be affecting me?
I also thought it was a recent Warframe update (as it's my main game), but they are saying they have resolved their issue, and I am still experiencing the lag on multiple games.

So...
Parts aren't overheating...
No large temporary files are left lying around...
At least some of my HDD has been defragmented.

This is my first time defragging this computer, and I have had it for just over a year now.

Thanks for any input, I will give any necessary information if I missed anything of importance.

 

[vvilltaylor]

So o successfully defragged most of my HDD.
I also set the cpu max/min to 100, but this put the temp passed Intel's recommended.
Used speedfan to see, well, speeds of the fans.
Turns out the front 2 aren't spinning.
They were pretty cheap, about $5 each, is there any fix for them or should I just buy new ones.