I don't think it is reasonable to expect that you can open any of these transmissions and not have to shim the shafts when you put it back together. Supposedly you can only replace the bearings that either feel notchy or loose but those have to be shimmed and since that is happening you should shim all the bearings. It is also reported that the factory did not do a very good job of shimming these boxes so if you are opening one you are advised to be ready to shim it before you put it back together.
Now you are replacing one of the gears? You have to shim the whole box. Period.
How many miles on this trans?