The Sense wire should go directly to the battery, not the output of the alternator!
Reason:
When you are charging there will be large current flowing from the alternator to the battery. (Large load [boost], means large spark and large injector PW, means large current being drawn...)
This current will cause a voltage drop across the thick wire from the alt to the battery (V=IR), say 50A of current is being used (50A should be coming from alt), and AWG10 wire (~3.34ohms/km) then the voltage drop is 0.5V over 3M (I'm not sure how long your alt->battery wiring is!).
This will mean that the voltage at the alternator end will be 0.5V higher than at the battery.
So the sense pin on the alternator will really be 0.5V lower than it should be!
(
calc)
The sense wire should be run directly to the battery. As the sense pin on the alt is high impedance it will take very little current and the voltage at the alt sense pin will be very very close to the voltage at the battery.
I'm not saying that this is the problem, 100%, but it is something that I would fix
Cheers
Wilbo
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