Surely, if the MM/ coda crankset is fitted as stock, the chainline will be ok?
The BB and crankset are matched, so it's not like a shimano square taper setup, where the user can screw it all up by fitting a 127.5mm bb axle on a crankset designed for a 107mm bb. This system was made for a 73mm shell or a 68mm shell, and that's it. Offchance, a 73mm setup could be on your 68mm cannondale, shell but back to my original observation, it it's stock, why would cannondale have done that?
Not to say you haven't done something correctly, but you haven't bottomed the bolts before the arm is all the way on have you? When torqued, the head of the bolt should be flush with the counterbore on the crank arm. if it's protruding, chances are the bolt is bottomed on the arm, and not up tight at all on the axle.
Any chance of posting some pics so we can help?