[Grounded63]

Those holes not lining up are probably 99% not your fault. That's just par for the course, with Import patch/replacment panels.

On my '63, I'm working on the drivers side. Inner/outer rockers lower A piller, front cab mount, ect. I've probably patched/welded up 75% of the holes. Then rescribed and drilled them once the panels were aligned properly. Import patch/replacement panels. Often just look similarly correct. But, generally still need to be tweaked. Or just plain finished, where they are missing correct details. To fit comparably to the factory panel they're replacing.

Looks great, with a full new floor in it !