I get wet passenger floors every time it rains. Makes me wonder if mine isn't leaking in the same spot. I don't know if you've done anything with the floor, but the corner where the floor ramp up also has a mound of seam sealer. That was the only spot of rust on the floors on my Cherokee.
'55 Willys Wagon, the original FSJ
Sitting on a '77 Cherokee frame, Dodge D60's
Isuzu 6BD1, NV4500, NP241