I read on their website that the 3650 has built in stops and that mrt recommends removing the stops in their shifter for the 3650.if you remove the stops is there any difference?
It's true that the 3650 has built in stops but if your power shifting best have stops on your shifter. Those stops won't take the abuse that the track will give your tranny. The only reason they recommed you don't use the external stops are some people aren't adjusting them correctly and doing damage to the tranny.
MRT has that shifter made for them and they pull the stop bolts. I don't know if it's a triax or urp unit but the UPR is only $144. Just make sure you adjust the stops correctly and you'll be in great shape.