If you are trying to use the 78-7029904 1 piece seals, those are for a coupe, not a fordor. You will need the 10' length of seal and cut to length, or cut down the 1 piece seals.
I am assuming the cross section of the rubber channel is OK, Is that correct?
Have you talked to Carpenter about the issue? Those seals should be the same as a '40. Some time back I did a '40 fordor and used the Drake seals. They fit perfect. The Drake part # is 81A-735139/1 and fit the 38-40 tip out style quarter window on a fordor sedan.
I have never installed a set of 1/4 seals in a fordor. I have however, attempted to install rear windshield seals (coupe) from Carpenter and they are way too big. Drake's fit perfectly.
I only state this as the possibility surely exists that the 1/4 seals are also too long.