904 1 vs 3 electrical contacts (2 questions)

I think the rooster comb on the linkage inside the trans has to be changed over to match the 3 prong switch.

Correct, part in the trans that operates the switch ( called rooster comb ) is different.
The earlier for single function switch can destroy a new dual function switch.
As for the levers and linkages to the trans, Yes there are a few different setups. Even the throttle cable from pedal to carb is different for 2 brl and 4 brl