Isolator is usually wired between batteries and not between the alternator and the batteries? Though with a 4 volt output on your main cable this is unlikely to be the issue IMO.
I don't really know the setup for a 2001, but on mine the alternator main power out cable goes to a junction on the side of the PDC and then jumps to battery positive. A side note, if yours does have the junction, check the nut for tightness.
Do you have a stock Denso alternator? That four volts on the main power out from the alternator sure sounds like a generator reading, if in fact that cable is isolated. But don't let me confuse the issue, just thinking out loud. The residual magnetism in the field winding magnets will give you four volts if the field current is interrupted, this is only on a true generator with field magnets, not an alternator.
How are you doing your tests, the engine has to be running. And how does it run on four volts? Something isn't adding up here or I'm confusing myself.