Lower Rear Quarter Patch Repair

Question: Is it OK to cut out the bad spots prior to having my replacement sheet metal on hand, or is it easier to wait until I've received the new parts?

I'm wondering how difficult it would be to line everything up with quasi-large sections of the body removed.
Not much harm in cutting off the rot areas on the quarters, you need to know if you need a skin or complete qtr. It will help a lot if you make sure that the doors and trunk lid are lined up as close to perfect with the qtr panels before cutting big pieces off, it will help you get the new metal lined up.