It would seem you have multiple issues. Also, a reminder that the bike MUST have a known good battery that is fully charged, in order to have sensible readings in the charging system. A low or bad battery will give test readings that will mislead proper diagnosis.
one concern is the low AC voltage from the alternator. Details are very important here. A misplaced test probe or test condition can give meaningless, undiagnosable data.
1. Place your DC voltmeter probes on the green and white wires at the regulator terminals. With the ignition on and the white and black wires jumpered you should read very near the battery voltage potential.
What reading do you get? ______
1.5 What is the reading directly across the battery terminals?_____
2. Discribe where, exactly, are your meter probes when when you measure the rectifier at 13.5v? _______
The rectifier output is directly connected to the battery terminals.
3. How could the voltage at the battery be any different? (Retorical) Describe where are your test lead probes?_____
**** Disconnect your battery POSITIVE terminal from the bike. Leave it dangling, unconnected to anything. ****
4. Use an ohmmeter to measure continuty between the battery minus terminal and the regulator green wire. What resistance do you measure?_____
5. Use an ohmmeter to measure continuty between the battery minus terminal and the rectifier green wire. What resistance do you measure?_____
6. Use an ohmmeter to measure continuty between the battery POSITIVE cable (not the battery) and the rectifier Red wire. What resistance do you measure?_____
7. Use an ohmmeter to measure continuty between the battery POSITIVE cable (not the battery) and the regulator black wire with the ignition switch turned ON. What resistance do you measure?_____
Also the harness at the rectifier becomes very warm when the rpm's are this high. Is that usual?
No. Are your connector contacts corroded? Do you see any signs of wire insulation melted? How about the harness black wrapping tape?