It's been a while since I last posted, but I fixed the issue. The secondary HDD may have been coincidence, maybe not. But what I did was take the GPU out, wipe the very minimal dust off of the top of it, and reseat it back into the mobo. No more stuttering!
I had two HDD's installed in my custom-built desktop PC, the 2nd one wasn't even in use. It was just a HDD that was leftover from my old PC that I decided to install so it didn't just sit around. Anyway, I never actually used it for anything. One day (two days ago) I hear a very weird clicking sound coming from my computer that I narrowed down to being that 2nd HDD. I couldn't open it in Windows Explorer, it would crash Windows Explorer constantly and would cause my computer to hang on the Shutdown screen without ever shutting down. So I removed it from my computer, the clicking sound stopped, confirming it was that HDD. But now when I run games, there is a consistent stutter about every second or so. Fallout 4, MGSV: TPP, Dark Souls 3 all stutter every second while Resident Evil 4 just constantly runs in super slow-mo whenever I execute actions (like running, walking, aiming etc.)
I've done tests on my main C drive where everything is saved, it passes everything. Health is at 100%, it never gets very warm, 0% fragments. I'm absolutely lost, I don't want to reformat since I lost my Windows disc and I'd have to buy a new one. Any help would be appreciated. Both HDD's were connected using a single cable with multiple data/power plugs on it.
OS: Windows 10 64-bit
Motherboard: Z77 Extreme4
Processor; Intel i5-3750k 3.4ghz
HDD: Western Digital Caviar Black, 7200RPM, 64mb cache