If you hooked up battery voltage backwards to the bike, expect the rectifier to have burned up, as well as the wires to it. Any of those wires routed through the wire harness also burned up wires running parallel to them. Get a wire diagram and look at the wires routing from battery to rectifier. Chase them physically, and replace all burnt wires you find.
Everything else should be ok if you didn't have the key switch on, as that would have prevented reverse polarity from reaching those devices. If you had the key switch on, anything with transistors in it likely fried when driven with reverse polarity.
You might want to review basic electricity relating to polarity of devices. Some lessons are more expensive than others.
Cheers,