I assume what the dealer told you is that the voltage to the sensors was 2 volts, not 2 amps, and that they should have a 5 volt reference.
If the alternator was putting out too high of a voltage it could have damaged the PCM, but before spending a lot of time and money on the PCM, I'd suggest you check some of the more basic things that could cause your symptoms such as a bad or dirty MAF sensor or, more likely, a bad spark plug wire or one that is saturated with oil due to a leaking spark plug well seal.
On the 3.0L SHO V6 it was pretty common for the seals in the valve covers to leak and allow oil to pool up in the spark plug wells. Over time, this will cause a misfire which results in symptoms just like what you describe.
Checking the front 3 spark plugs and plug wells is pretty easy and straight forward, but the rear three are a bit more difficult. It's been awhile since I did this so I don't recall the specifics, but it seems like there was some plastic cover that needed to be removed and maybe even the IAC solenoid had to be removed to get to the rear wires and plugs.
-Rod