An issue I am seeing now, is that something people neglect to see, but turns out to bite them HARD is where the floorboard overhangs at the door opening. In the end, that seam has to be perfectly smooth from the back of the seat clear to the door hinge side. That Lip needs to be smooth across the whole thing.
Dont think you can figure it out later. push the panel so that the lip is in line, THEN deal with the fact that your transmission cover will be short. Thats easier to deal with, then that lip not lining up. Am I making sense? Done two 50 floors and that is one mistake I will never make again! The problem is, the panels you purchased that many years ago were too long. Your first pic shows the problem in the lower left. I would hope they fixed this problem by now, but I doubt it, since these cabs were not uniform by as much as a 1/4 inch in the day.
The remanufacturers struck a balance and this is where its up to you to decide where you want to cut that panel in half if its not fitting right.
So, take both floorboards, put the transmission cover on and tighten securely. IF the lip at the door overhangs too much, you have a decision to make. I chose to just rip the transmission cover in half and very carefully take 1/4" off the cover. This was mostly because the master cylinder hole was in the right place when shoved against the door lip, and so was the battery box on the other side. Make sense at all? If not, GOOD for you!