I got the sides mixed up and should have referred to the side nearest the transmission. After looking at your pictures I think I see were the problem might stem. It appears you kept the L brace near on the transmission side of the new floor whereas I took it off. I think the using the L brace would have pushed the joggle in the floor support out further and made it clear the step. I didn't maintain the L brace because the new floor panel isn't two pieces so there is not flange to weld it to at the front like you have. It appears you added the flange to that location which is pretty cool! I noticed you kept the old battery frame and now it make me wonder if I should have.....
Even with the L brace I still have a heck of a gap, the tabs on mine have to be pushed out a fair amount to make contact. I was thinking of shimming the gap with some sheet metal so the tabs weren't so angled.

I will take a picture of what I have in the morning. Thanks everyone for all your help! This is an awesome forum!!!
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1950 Chevrolet 1/2-Ton 3100