Broken Taskbar Links, Missing programs and folders. Virus? Help!

Ok will do, thanks for trying to help!

I'm going to go ahead and wipe the secondary HDD as well being that it is nearly empty and I just want to do a completely fresh install. With that in mind, do I have these steps correct? Anything else to know?

1- Burn Win 7 SP1 ISO & Media Refresh to USB via Clean Reinstall - Factory OEM Windows 7

2- Wipe data HDD with "clean" diskpart command and unplug Disk - Disk - Clean and Clean All with Diskpart Command

3- Wipe SSD with "clean" diskpart command (same as above)

4- Reformat SSD and do a clean install

5- Reinstall AV & other programs

6- Make a damn Backup image so I don't have to do this again!

Yes, I move user folders and install steam and games on the 2TB data drive. If I were to wipe that drive too though, should I do that after a fresh install?

Or can I wipe that drive first, unplug it, then wipe the ssd & install?

Thanks again, here we go!

I should just use the "clean" command prompt right? Not "clean all"?

Alright, well only a couple hundred more updates and fresh Windows 7 is all ready to go!

So now I'm curious, is there any way I can be any safer using this PC? If this really was the result of some sort of virus or something, is there any other software I should have?

I already have MSE, malwarebytes and SAS, and I use a few tracker blocker addons with chrome