Update your usb drivers to see if it helps resolve the usb issue. Latest usb driver for your motherboard can be downloaded here.

Sajin
Update your usb drivers to see if it helps resolve the usb issue. Latest usb driver for your motherboard can be downloaded here.

Didn't change a thing.
 
I can't believe after all this work I'm actually worse off than where I started.

DrPhD
I can't believe after all this work I'm actually worse off than where I started.

It happens. Next best thing to do would be to do a clean install of windows. If you continue to have problems after the clean install of windows you'll know it's a hardware issue.

Sajin

DrPhD
I can't believe after all this work I'm actually worse off than where I started.

It happens. Next best thing to do would be to do a clean install of windows. If you continue to have problems after the clean install of windows you'll know it's a hardware issue.

Well I'm going to need a very detailed guide on how to do that without losing anything that I want to keep and without ruining the entire way I set up this PC across 3 different hard drives.

I'd simply disconnect your old drives and install a spare one for testing purposes.

Sajin
I'd simply disconnect your old drives and install a spare one for testing purposes.

I don't have spare hard drives laying around.
 
I have an SSD with my OS and downloads on it, a 1TB drive for my games and a 2TB drive for my media.
Now I just have to figure out how to format the SSD and reinstall Windows 7 on it while not losing any settings or programs and making sure the other two drives work perfectly with it like they do now in terms of which folders go where. (E.g. the entire my documents folder is on the media drive.)
 
To do this I have no other computers, hard drives or a smartphone. The only other storage device I have is a 256MB USB stick.
 
 
Makes me wonder if I should do win10 instead or if I should wait for the new PC. But then I don't have the drives to actually save everything.

If you have just the os & downloads on the ssd then you can simply move all your downloads to your game/media hdd to save them. Re-install the os on your ssd and you'll be good to go. Your my documents folder will be clean on the fresh install but it won't matter as you have everything saved on your other two drives.

Before you go all out and do a OS re-install - I would check all your cables.  I mean all of them.  Check every single one from the USB ports to the mobo, all PSU and power cables, SATA cables, everything.
 
Then remove and re-seat the graphics card.  Remove each RAM module and re-seat them.  Make sure every single thing is plugged in properly and snugly.  This may fix that USB sound of connecting/reconnecting a device.  I've seen this before.  
 
And lastly check to see if your mobo has a BIOS update.  This also may help or solve some of your issues.  Just be careful and take it slow if you do this.

hapkiman
Before you go all out and do a OS re-install - I would check all your cables.  I mean all of them.  Check every single one from the USB ports to the mobo, all PSU and power cables, SATA cables, everything.
 
Then remove and re-seat the graphics card.  Remove each RAM module and re-seat them.  Make sure every single thing is plugged in properly and snugly.  This may fix that USB sound of connecting/reconnecting a device.  I've seen this before.  
 
And lastly check to see if your mobo has a BIOS update.  This also may help or solve some of your issues.  Just be careful and take it slow if you do this.

I just can't seem to pinpoint which part exactly is causing the issue. Or why it started happening once I reset the CPU clocks. I wish the PC itself or the error report would tell me something but...
 

What does the Device Manager show?
 
Do any of the devices show the yellow warning symbol?