Great Stuff i am doing a similar project (also much worse than i expected) the first Challenger i bought in similar condition placed it into storage while i done a second TA just getting back to it after 4 years ,how do the rear stiffening bars fit the new floor pan.
Looks like the water come into your big block through an open valve
Measure ,measure , measure.
The digital spirit levels you have work well just as well as the floor is flat
Ensure the metal & welds at the front frame rail firewall & front floor supports are good as it is a pivot point for the front rails as they do flex some.