Well, I don't think it is due to the lithium battery, as it is fully charged, and when the regulator sees 13.4vdc, it will cut the output to the black wire to the field coil. The better way to check alternator output would be to disconnect the black reference voltage wire, and then check the output of the yellow wires. Remember, this is an electromagnetic alternator, not a permanent magnet system, which would put out full AC voltage when it is running. On permanent magnet systems, you should measure from 30-70VAC on the yellow wires. On our system, full VAC will only be measured when the field coil is fed with a full 12vdc from the battery. Your system might actually be functioning ok, you may not be aware of why it isn't putting out full VAC. You might need to feed the black wire with 12vdc,or leave it disconnected... can't remember lol. I am sure someone will give you the correct procedure.
Charlie