Arbiter Odie, what you describe has happened to me in Windows 95 days, I found out the hard way about it too, but I did something about it then and it is the solution that works for me today. After getting sick of modifying Windows 98 for four days straight then having it break on me, then four days again.... I asked myself if only there was a way for me to get things just right... then freeze that moment in time, in some sort of... an image...
that I could then... reimage... and have things be the way I want them to be... always
So today my Windows 8 reimages in a couple of minutes and I reimage all the time. So partition your SSD, install Windows on a relatively small partition, move your Desktop, and personal files elsewhere, install large apps on a different partition then maybe install a dual boot and image one OS from the other in two minutes. You can perfect your image over time... I actually have a txt file where I write the changes I need to make every patch Tuesday when I image, update, make changes, make a new image. I save certain old image files on another hard drive just in case anything goes wrong.
That way WHEN, not IF.... WHEN something goes wrong I can identify the culprit easier. Latest Classic Shell version has been out for a while and it does not cause problems of the nature you fear...
Stop reformatting an entire drive, learn about partitions and the wonderful world of 2-3 minute OS partition reimaging!