Could be all kinds of stuff, nothing would narrow it down quicker than a good scanner to monitor the sensors when this happens. I'd be watching the IPR valve maybe, you could give it a look to see if the plug & wires look intact and that the "tin nut" hasn't fallen off the stem. You never get an SES light?
On the electrical side, could be a bad connection somewhere, especially with the windows & radio issue BUT, the VSM is just the "Body Control Module" and shouldn't be doing much to the engine.
You talk about "tapping" it though,,, behind the Radio? That's where your VSM is located. You're not talking about the PCM? Behind the Fusebox?
If so, and you have a Tuner attached, I'd take that off. A bad connection to the board does strange stuff. Take it off in any case and see. Also, because it's an '02, have a look at the connector that feeds the fusebox and makes the transition to fuseable links. It's under the hood, next to the airbox, attached to the top of the fenderwell, under a cover marked "Caution High Current" and about 1sq". A corroded connector there also does strange electrical things