I think you are right about the planetaries and reverse drum. Do you know what year the 4R100 is?
1; The pump will be higher capacity on the 4R100,
2; The center support in the E4OD might have a bushing, while the 4R100 should have a roller bearing. DO NOT REUSE THE BUSHING STYLE!!! It was an unbelievably crappy design. If the center support for the 4R100 doesn't fit, then get an upgrade kit instead. Its worth the added cost (if you are really stuck I could try and mail you a used set I have).
3; Depending on the year and build of the 4R100, it will probably have steel carrier planetary gears, but they may only be 3 pinion. Your transmission might have 4 pinion aluminum, so a swap in that case would be a bit of a trade off.
4; the planetary gears have thrust washers on the older E4ODs, where the 4R100 should have an actual roller style thrust bearing. The ring gear hub was also revised to accomodate the thicker bearing so that has to swap over as well.
5; Generally the sprags and one way clutches are better in the 4R100, but not all of them are backwards compatible. You'll just have to see what fits.
6; Hmm..... it seems you can change the case fittings for the cooler from 5/16" to 3/8". I might do this for mine since its in the shop right now anyway. This option goes all the way back to 1990 so anyone with an E4OD can do this
You will have to be VERY careful with these swaps to make sure that they will work correctly after everything is put together. Check the clearances, fit and function of everything you plan to change to make sure they are correct before putting the transmission back in service.