So it kinda sounds like the imitation thing was still happening in '69 when Toyota came out with the J30 3-speed, as you are suggesting that the FJ25 bellhousing is different in bolt-pattern.
I don't recall using a spacer with the swap. The Toyota J30 input shaft is actually longer according to:
SM420... It is a wider (longer) pilot bearing that supports the SM420 input shaft, no?
So, the Toyota J30 came out in '69, and the non-military-exclusive-SM420 was available from '47 to '67.
The Novak Guide to the GM Muncie SM420 Transmission Interesting.
BTW, the floor-shift Toyota 3-speed shifter was a fine match for the SM420 after I bent it to clear the roll-cage and aftermarket center console.