The battery to frame ground connection is under the tank. It uses the rear frame bolt on the voltage regulator, I guess that is the black wire you see going under the tank. From what you say, sounds like your battery was not connected !!
As long as the frame (as above), the battery negative terminal and the -ve terminal on the rectifer are all wired together, the electrical system will work correctly. Doesn't matter how the wires run. If I remember correctly, the original black wiring from the -ve battery terminal doesn't quite match the arrangement shown on the wiring diagram.
There is a second connection to the -ve terminal on the battery and that is the black/white wire coming up from the alternator, as shown on the wiring diagram.
Hope this helps.
