You could be right it could be a difference in the meshing between the fd and mainshaft gear, if the fd has been changed then the mainshaft needs changed at the same time
Although if the mainshaft is not meshing properly with the FD ring gear it will be very difficult to turn them together freely
Its very hard to diagnose the problem without being there to have a look at the gearbox, it could be something very simple that you have missed out. It takes you to build them a few times to become farmiliar with some of the problems that can happen when swapping transmission parts