Chuck, I just dug out the scale wheel conversion set that I ordered for my 1st run Erie Lackawanna U33C back in 2012. I never installed them and they're still in the original packing.
As you guessed, the 6408142625 part number is indeed for the first run of U33C locomotives.
To be honest, I don't think anyone in Parts is aware that the gear ratio was changed between the first and successive runs and I'd wager a part number for a "new" U-Boat 6-wheel scale set for the latter doesn't exist. Frankly, given the "scale" buyers are few and far between, I don't think there will be much motivation at the Circle L Ranch to create one.
As I mentioned in another post, I think that even once the scale wheel conversions for the SD70/ES44's run out, there will be no more. I would love to be wrong with this theory.
Rusty