Not sure why you're saying you need to replace the stem...unless you're just looking to change the length and/or angle of it. Having only ridden flat bar bikes a few times...it has always been my understanding that they are a road bike...just with flat bars instead of drops. Obviously brake and shift levers are different. As such...you shouldn't need to replace any derailleurs/brakes. However...as you indicate...you'll have to change to brifters. Something you didn't mention...which I'm sure will be effected...is brake and shifter cable length.
Dan