It will depend greatly on which Allison you choose. I've crawled under the truck with a measuring tape. With any of the medium duty Allisons 2000 & especially 3000 series you will have to remove/relocate the crossmember.
The second big issue is the width of the Allison. They are large, round cylinders. The front driveline may not clear the larger models like the 3560 since the front pumpkin is centered. The 2000 series might, but they don't have as low of a first gear. The 3560 with a high torque ratio converter would actually have a deeper granny gear than the stock Deuce. Perhaps if someone were insistent on installing a 3000 series Allison they could make a two-piece front driveline that swings sideways to a carrier bearing with CV joints, mounted to the passenger side of center. Since the front axle is mostly used at low RPM that might be a viable solution to clear a big Allison. But I don't know who would be crazy enough to try such a solution
One could also have a chop shop make a custom Rockwell front axle with a pumpkin shifted to the passenger side. But that would be $$.
The third issue is the depth. The tranny would hang much lower than the Spicer. If an entire drivetrain swap were performed, you could raise it a few inches for better ground clearance, at least up to the constraints of sheet metal/linkages.
A fourth issue is the control module. All the newer Allisons require computer programming. There are stand-alone ecu's for the 5 speed Allisons. But I have yet to see one for the 6 speeds. You would have to know someone who can tweak the 6 speed programming to optimize performance behind a multifuel.
A fifth issue is the flex plate/starter. To keep the multifuel engine you would need to find or custom make a flex plate + starter. The bellhousing should be okay.
A sixth issue is double overdrive. The 6 speed Allisons have overdrives in the neighborhood of 0.65. I'm not sure if the multifuel has the horsepower at 2500 rpm's to maintain speed without lugging, even with the directly locking converters from Allison.
A seventh issue is a tranny cooler. You will have to plumb a cooler up front. If you live in a hot climate that could mean trouble for overheating in the summer b/c the radiator in these trucks are rather small comparably speaking. But on the + side, All the Allisons are easily adaptable to tranny retarders. So if you worked out a good transmission cooling system you could install an Allison with a retarder. Your braking ability would increase significantly. And the wear/tear on the stock brakes would go down significantly. Some people poo poo tranny retarders, claiming they overheat the tranny fluid. If that were so, then city busses would be exploding trannys left and right. I think retarders in these trucks would add a significant safety factor. It would be nice to find a used Allison that already had a built-in retarder. Your bus tranny might already have one installed.
In the end, it might be well worth the money/effort to say goodbye to the multifuel engine & go with an already-bolted-together Cummins/Allison combo. That way you would have no flex plate, starter, torque converter, or ecu issues. There might be room to pull the Cummins/Allison forward a few inches to save the trouble of relocating the crossmember & transfer case. Certainly if you went with a slim-line electric radiator fan you could lost the belt driven fan and pull the engine forward several inches. You might stll have front driveline issues. Would the transfer case handle a Cummins? I don't know. I say go for it. If it explodes then replace it with a better transfer case.
Anyway, sorry for the long post. I hope that I've helped to stimulate some ideas.
