[haybaler]

"black goes to neg."

Yes, black goes to ground. If you connect the black wire to the positive side of the battery, sparks will fly, possibly cause wire harness damage!

Don't do that!

Your regulator looks like the one from earlier model Yamaha, TX500, uses 5 wires instead of stock XV535 rect/reg that uses 4 wires.
No big deal, just replace with the correct reg/rect, or connect black wire to any ground, then check charging system with voltmeter.

 

[haybaler]

Wait a minute!

The TX500 unit is only a rectifier; the TX500 used a separate regualtor, so it's really not the right part. Suggest you replace rect/reg with correct unit.