For an FXR its a little different
Tranny into frame and mounted to the swing arm and isolators,
Primary mounted to tranny,
Engine into frame and primary.
I just snug the primary/tranny bolts at first, and then go back and lock them down after I have the motor in. If only the motor was out, then no need to do anything back by the trans. You can slip the motor in and out without taking the rear sprocket off.
There's nothing to shim and no tranny to frame on an FXR. The tranny just floats on the rear isolators and bolts to the primary and rear of the motor case. If the case and tranny don't line up, then you'll need to find out why, shimming is not advised. Usually it's a sprung inner primary, happens after the rear engine mounts crack.
After you get it all back in, you'll need to align it with the turn buckles.
Last edited by Thermodyne; 05-22-2013 at 08:58 AM.