Doing a bit of on line "search" it would appear the Euro 2 is the basic exhaust emissions standard for all bikes up through 2006. The CE label has to do with electrical emissions which became somewhat of a concern in the midst of it all. My guess is the 2 ECU are the same, just differing certifications.
All the early MV were Euro2 compliant. 2007 saw the switch to the Euro3 and also a change to the 5SM ECU (some late 2006 models also got this ECU).
USA spec bikes (with the exception of a very few first years models) also received a CARB evaporative emissions system. That system has nothing to do with the ECU on the MV bikes, though.
Maybe someone else has better information, but I think the 2 you are looking at will be the same.