Is the cab on or off the frame?
There are a number of variables in the problem and they all multiply the number of possible fit problems.
Replacement panels can be made by different companies out of different thickness material and bent or fabricated to different tolerances. Use 2 or more together and the differences add up.
The cab it's self has shifted it's shape over the years especially with rusted out panels.
If I'm doing a frame off or repairing with the cab in place, I always fit and tack the new floor and mounts in place with the cab on the frame, doors on and closed, and use the frame mounting holes for alignment. The only alternative is squaring the cab shell with a lot of measuring and welding a lot of temporary cross braces inside the cab.
Jack and shim body until everything is square.
Cut, bend and grind new panels until everything finally lines up.
I often pop rivet some of the flanges together for temporary positioning before tack welding and use a lot of clamps before I fire up the welder.
Personally, I use a spot welder as much as possible for floor panel replacements.
