It really looks like you're going to need some patching on the lower before you put the floor down. I spot blasted the lowers part you're talking about in mine , treated with Ospho, then epoxy primed. Drill/ prep the floor pan, lay it in and use a spot drill bit in holes you put in the pan to clean the lower panels. It's a blind area once assembled so you want to minimize bare metal as best as you can. One other suggestion, You don't need to drill slam through, you're only drilling to to remove the upper panel, You're making a bunch of holes that are unnecessary on the inner rockers and such.