Before you dive in, what exactly is backed up from your OS drive? If you have a drive image from when things worked fine, I would start by recovering that and see what happens(that's the beauty of drive imaging). If it really comes down to starting over, here's my method:
1-Install and tweak OS
2-Install iLok and Pro Tools and AVID plugins(always using the right-click>Run as Admin option for Windows) and test a few sessions(3rd party plugins will be inactive and that's okay for now).
3-If tests go smooth, save a drive image(name it System Basic Load)
4-install plugins(but not VI stuff yet)
5-test for solid function. If all is good(run some recent sessions), save a 2nd drive image(name it System with Plugins)
6-install VI plugins and sample libraries(or re-link to existing libraries)
7-test with VI's(you will likely have gone thru some fun re-authorizing anything that doesn't use iLok). Assuming things are working well, save a 3rd drive image(named System Complete)
Now, if some future catastrophe hits, you have 3 images to recover from(feel free to name images in a way that makes sense to you
). I would also save an image every few months(assuming the system is running well) and image BEFORE adding any new software or update. I rotate a pair of matching system drives so whenever I do an update or addition of new software, I clone the C: drive>swap the fresh clone into the machine and update that. If things go sour, swap the original drive back in so I can work(and solve the problem when convenient). If things work dandy, the old drive sits in the drawer, ready for the next repeat
BTW, since you are recovering, you might as well change the CR2032 battery and re-check/update BIOS/UFEI
