You're quite right about the spigot end of the input being too large. When I used a donor 63L short series box to replenish my completely fisted 63A, we had to turn down and shorten the spigot end of the input. The factory L series spigot OD, is bigger than the OD of the factory A series spigot bush. Turing it down however was challenging. If you hold the input shaft in you hand, you'll see that there isn't much to hold it by. Mine had to be held by forcing the tapered synchro ring journal, into a tapered socket in a mandrel to it could be turned.
Although i supose if you had a big enough lathe chuck, maybe you could tighten the jaws up and leave the gear part of the shaft on the chuck side of the jaws. depending also on how deep the jaws themselves were, and if you could make the shaft itself run true when holding it on the splines.
As for the clutch situation, the plate for a 63A box should fit with nthe standrd cover. BUt I'm a huge proponent of the 200mm flywheel modification. (Plus I get mine done for free

)
I would imagine that relocating the starter motor could be quite a mission to get the starter pinion to mesh correctly. What about grabbing a billet of steel, and making a copy of the L series flywheel, only with the A series crank bolt pattern? Then the L series ring gear could be reused. (And you could drill it for any clutch patern desired)
I don't know what steel costs nowdays, but back in Late '98, I got a billet of steel to make a 13B flywheel for about $40.