The trans mainshaft was extended when the e-start alum. primary was added, 1965. It was extended again when the alternator was put under the engine sprocket in 1970, and gawd knows when else. You can find out by the dash-year numbers of the various trans mainshafts. There's a -41 that goes back to kickstart, a -65, a -70, each one a little longer than the last. That will determine where you end up, left-right.
What I want to advise you is that the front Knucklehead engine mount pad is 3/8" higher than the Panhead. Knuckles or UL Flathead motors mounted in Pan frames require a 3/8" spacer on top of the frame, under the motor mount, across the front. Ignore this, and once tightened down and run, vibrated, the front motor mount will snap off the Knuckle engine cases.
What I want to advise you is that the front Knucklehead engine mount pad is 3/8" higher than the Panhead. Knuckles or UL Flathead motors mounted in Pan frames require a 3/8" spacer on top of the frame, under the motor mount, across the front. Ignore this, and once tightened down and run, vibrated, the front motor mount will snap off the Knuckle engine cases.