the built in speed controller cant power them then
This!
He's right, the stock Tyco transisters for the speed control are just strong enough for the stock motor. As soon as you hook up a mod motor, it cant handle the larger current draw and over heats the transister and burns them out.
Yes. It shouldn't be too hard to replace the MOSFET's used in the stock electronics with modern higher current pieces. Electronics aside, the real limitation is the gearbox. Tycos stripped gears left and right with the stock motor. Imagine what an aftermarket motor will do to the gear box.