The two crankshaft types are really only tied to whether it's a pullstart engine or not. An SG shaft won't have a pullstart (closed backplate) and a IPS shaft engine will. IPS is Traxxas' abbreviation for Integrated Pilot Shaft which just means it has the little nub on the crankpin for the one-way clutch to drive the crank.

Ive be seen some engines with a longer crankshaft output than others which can require cutting the end of the shaft off. Likely this is not the issue here. It sounds to me the OP removed the tapered collet before installing the flywheel.