I'm close to the point where I'll be installing my rear floor pan, and will be installing it similar to the way it was built at the factory, that is, it'll be sandwiched in between a couple of layers of sheetmetal. The question I have is, how do you go about preventing corrosion between the pinch joints? The factory seems to have pre-painted the various sheetmetal components before they were spotwelded, but I'll have to take those parts down to bare metal so I can get a good clean plug weld with the mig. Would this be a good place to use the 3M weld through coating?

Randy this would be an excellent spot for the weld thru primer. You do want all areas that will be welded clean as possible. The way I apply weld thru is that every piece of metal that will touch another piece gets coated. So I would coat the inner rocker,both sides of the rear panel and bottom side of the quarter support. Once you have everything welded a good thing to do would be spray some cavity wax around the area from the inside of quarter support thro one of the acces holes. That will help seal up any spots