Hi Charles,
Yes, the fuel injection housing/assembly will interchange as a whole unit. Timing is by offset drive tang and slot.
Set the engine up to #1 firing position and pump lifter position and also so you can check flywheel timing. There should be assembly marks on the crankshaft flange and the flywheel but it pays to check when interchanging. Check that the timing mark on the perimeter of the flywheel is visible through the cover plate window on top of the bell housing. If all is right when #1 piston is in firing position, injector pump lifter is at or near top of stroke, flywheel mark is under the timing pointer and flywheel marks all line up.
They did use several different flywheel drillings for the twin disc clutch, the rockford clutch and the open style dry clutch. As far as I know the crankshaft mounting flanges were all the same.