I'd think that the differential gearing would be more important... you're not benefiting from getting a diesel manual transmission otherwise, if the differential is skewing all those ratios different. Of course we don't really worry about getting a particular manual since there simply aren't any diesel manuals around here.

Any crankshaft differences are minor, looking at the 603 crank it looks like it can take a pilot bearing, of course as you heard the later 617's had an annoying slight difference which was apparently solved by just freezing the bearing so it would fit. I'm not sure if the 603 has this slight difference as well.