If you make a point of getting the electronics with the engine (black box computer, etc) all engines can go into any frame.   Older engines are 4 speed but the 4 speeds match up ratio wise to the same top end speed as the newer engines.  

Newer engines have better starter motor set ups compared to the very old engines.

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Your problems can come from mix and match,  i.e. the wrong electronics on the old bike for the new motor you just got.

Most folks breaking down a wrecked bike will send the electronics with the motor if you request it for a moderate extra few dollars.