"If I want to eliminate the motor, can I take the Primary chain system off and start the bike?"
Well you could but it would require a starting cart..
Remember the primary chain need to be present so that the ring gear can drive the clutch side chain.. You could start the bike and pull the side cover(drain the primary), should be able to hear the sound real good if it's in the primary.
You can also use a mechanic's stethoscope (sp) and listen for the sound. The sound might be coming from the balancer chain?
You might want to pull the rotor and make sure nothing cam loose in there.
Good luck,
Bruce