"Does the VR raise the voltage going to the alternator?"

I readily admit that I have not paid much attention to how the automotive VR works inside, but it needs to alter the voltage to the alternator field in order to control the output of the alternator. If the VR was only able to trim the battery voltage then it would not be able to increase alternator output when the battery voltage was low. So in answer to your question, the VR *can* raise the voltage going to the alternator field.

In your experiment the engine was not running and the voltage was at 11.9. Given that the VR is designed to keep the system at 14.5V, it makes sense that a higher voltage would be presented on the field circuit.

In my opinion, the MSD by itself is not causing the problem, although it still makes sense to do the test you described (in an earlier post you asked why to disconnect the heavy red from the battery before the test; I would do this just to be safe). I run a 6AL-2 and do not experience anything like what you describe. In my car I could notice a definite difference in the load on the electrical system after installing the MSD because my ammeter is now always a bit farther on the charging side (ie alternator is needing to deliver more current due to the extra load) as compared to when I had a chrome box on the car.

I don't have a great suggestion at the moment. I continue to think that there is some sort of high resistance short somewhere in the system. You will likely just need to take a very methodical approach to debugging it. One thing you may want to consider is pulling every fuse that is not absolutely necessary. You could also jumper over the ammeter with a heavy gauge wire and just use the analog voltmeter to see if the condition persists.