I've had one engine with MK3 cases and an earlier crankshaft. It was the ex-Martin Adams Commonwealth race bike. It had two aluminum shims, one in each side, between the crankcases and the bearings, to make up for the difference in crankshaft width. If I recall correctly, the shim on the timing side was thicker than the one on the drive side, maybe to make sure the oil seal was properly located on the crankshaft. It worked fine. In your case, it all depends on what sort of primary you plan to use. You haven't said if you plan to still use the MK3 primary components, in which case you need to keep the MK3 crank as L.A.B. said, or an earlier primary, in which case you need to machine the MK3 crankcase to match. If you plan to use a belt drive and custom cover, you can do it either way. But if you do that and still want to keep the alternator, you will have to fab up some sort of way to mount the stator.
Ken