Lower Rear Quarter Patch Repair

Aftermarket parts fit like crap. Original parts fit like crap. Your chosen method of replacement is unorthodox.
At some point you just need to start tacking and beating things into submission. Be prepared to un-weld some tacks. I do admire your enthusiasm. This is a huge project. You will be using copious amounts of filler to make it look right. Nothing wrong with that if you use proper techniques.