Windows 7 & Programs frequently stops responding for 10 - 30 seconds

UPDATE: I ran the System File Checker and it got to about 79% and said "Windows Resource Protection has found some corrupted files but was unable to fix them". It then pointed me to a CBS log file, but this thing may as well be greek to me, unsure how to proceed at this point?

Starting in the past week sometime, Windows 7 has begun behaving a bit oddly. When it runs, everything seems to run at optimal speeds, but very frequently it stalls up and programs stop responding (freeze up, have the glossy white overlay) and then resume after about 10 to 30 seconds. This seems to happen on all programs, internet browsers, video players, image viewers, Steam (haven't attempted to run any actual games), even windows explorer itself will do this sometimes. It typically happens when I interface with something like trying to scroll through a website, or right-clicking open a shell menu, with folders I often get loading bars like it's having to reload the folder, on videos it frequently acts like it's trying to catch up with buffering, the video lags frequently every 10 seconds or so and has image distortion (I use VLC Media Player)

So what I've done so far:

-Used a system restore point back to before when I am sure the problem started.
-Ran a checkdisk scan on my primary drive (no issues)
-Deleted all cache files for browsers and the like
-Uninstalled a few windows updates that occurred this past week
-Ran Windows in Safe Mode

During that last step, in Safe Mode I have none of the issues present when Windows loads normally, it performs at the speeds expected with no program freezing. I have tried looking at Event Viewer but honestly have no idea what I'm looking at there.

One known issue that has occurred this week is during one of the windows updates, it had apparently stalled at 15% and remained that way for several hours with no activity, I left for work but we had a power spike while I was gone and the system lost power, Windows attempted to recover the update process and I'm unsure if this may have messed up a critical file or not. I also don't know with certainty if the problem began before that or not.

I seem to recall it having the stalling problems before but less frequently and severe. Last weekend I recall playing a game which started to slow down at certain intervals but wouldn't hang up or crash, just slow down. I also have had some of the freezing issues before with my browser but a lot of it was related to add-ons which I've removed or replaced and having way too many tabs open.

So just curious what my next steps should be? I've tried all basic trouble-shooting I know of but not sure what to try next. My hardware seems to all be working properly as near as I can tell and no issues with safe mode.

My Specs:

Windows 7 Pro SP1
ASUS Maximus Hero VII Motherboard
Intel i7 4790k CPU @ 4.00 GHz
16GB RAM (I think DDR2)
GeForce GTX 970 GPU

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