The actual differences between the cr and mt are too numerous to list, however, there are some things in common. Back in the mid seventies, I ran into a guy out riding that had put a cr125 top end on an mt125. There was something really cool about that. I have since read or heard that the cr top end will bolt right on, so it probably wasn't an illusion. If it were me, I would watch Ebay for a cr jug and carb, and a new piston. I think that would be preferrable to porting the mt jug. With the cr jug, you will need more carburetor for sure.
As far as using a cr pipe, those old mx bikes were louder than the space shuttle. Your neighbors and others may not be too keen on that. You might be better off trying to find a period aftermarket pipe like a torque engineering pipe, since it will bolt up in place of the stock pipe. The mt was underpowered, so porting and fitting a cr pipe will most likely give lots of noise, and a slight increase in power.
Of course it's your decision, but having been involved in a couple of projects like these in the past, I have found that the only 2 choices are to do it all right, or not at all.
