If you choose to go with all knuckle couplers instead of a transition car, you can buy under shank and over shank couplers that will give you different coupler heights.
You can also remove the couplers from the trucks and get couplers with pockets to body mount them.
There are also things called talgo adapters which you can use to put knuckle couplers in the truck mounted coupler slots.
Bachmann sells couplers but they don't have the conversion options that Kadee has.
https://www.kadee.com/hocc_tyco.htm