| Apart from the amount of gears already mentioned
the Early ones have a standard type clutch and later ones come with the APTC clutch.
Electronics wise the early ones don't have the neutral feeding into the ECU where as the later ones do as part of the start interlock system.
Although your not stuck with Standard ECU as there are Options
Such as
Standard ECU reprogrammed (setup on a Dyno by either CJS or BSD) and the IMMO removed so you don't need coded clocks or a key, if going this route I would change the TPS for a Linear one
1.5M ECU such as Andy Challis uses, limited to about 8500 rpm by the rev-limiter. Although these can also be reflashed (Direct Link software and key) and the rev limiter moved as per the one on Dallas's bike. As the 750SSie uses the same stoke as the 620 your better off using its ECU than the one off the 900SSie
Another option woulld be the good old 1.6M ECU as used on 748/916/ST2
with a EPROM programmed to suit, as the 748 Shares the same stroke as the 620 I'd go with a 748 chip for the ignition curve
Also after market units such as Nemesis and FIM can also be used
On my spare bike I'm currently looking at using a 998 ECU with the 750SSie Injectors as that ECU knows nothing of coded clocks and runs a normal rev counter, I make it about 11% that I would need to reduce the fuel by using a Power commander
Checkout the Desmo Due Paddock on Facebook | 
skidlids
Threaded Mode