Not unless you have a super rare prototype motor where the exhaust went out the front. All production Cannondale motors are physically interchangable. The only differences are subtle from motrocycle to quad (like gearing and throttle body differences). What do you got?
There's a few little things like valve cover fittings if its from a bike or cable /hydraulic clutch ,stator wires but the good news is they all can be made to work. If you have a 500ecm you will need to install a aluminum valve cover ,500ecm exhaust cam and cam sensor if it doesnt have one. Or switch to the 1000ecm and wiring harness.
If its a true fx400 original the case will need the main bearing bore on the flywheel side modded to work with the newer crank. A sleeve is installed and the depth is machined down for the smaller wider bearing that the newer cranks use. A new oil grove will be needed as well. Timbo can do that for you or any competent machine shop.
I was eyeballing that bottom end too but I found the case I was looking for... While we are on the subject what was the difference in the displacement of the 01 fx 400 and the 02 432? Size of the piston kit I would assume but is the stroke the same? Ray