Slant 6 balance

Just to verify the valves and ignition for each cylinder is ok, I would start it up and pull off the plug wires 1 by 1 and see if any dont change the roughness more. If so, that cylinder isn’t firing. Hopefully the cause is nothing real bad like a broken rings, piston, bent valve etc. As far as the possibility of being out of balance from the wrong parts is very unlikely. Pishta brings up an interesting possibility that the flywheel center hole may be the large one on a small hole style crank that happened during the engine swap.
If the plug wire thing doesn’t show any evidence, I think your time and money would best be spent pulling the bell housing back and look for anything obviously wrong, loose or damaged or off-center pressure plate, disc damaged, bad throw out bearing, wrong pilot bearing and including that flywheel crank interface mentioned above.

please keep us posted on your progress.