Hey Gang,
I've been following these posts, and this whole thread has been entertaining. Richard, you've pretty much covered all the bases regarding what's been going on here, and yes, you are almost spot-on about the V2.0 upgrade. That upgrade came about because of a few bugs in the original release of the MP-1. There were a few parameters which didn't react well if you went over certain input levels and the MP-1 would make a couple of really unpleasant noises. So they got those issues tamed down in V2.0.
The fact that it coincided with the release of the "Vintage" Split-Stacks was just timing. In the late 80s, more players were talking up a storm about earlier Marshall speakers sounding much warmer and (in their opinions), better than the speakers Marshall was putting out at the time. So in response to this, Dave Tarnowski and Co. started measuring EQ curves from these old speaker cabs and came up with a small EQ filter circuit that they started putting into the Split-Stacks and named them "Vintage" split stack cabs. The truth is they still had the same budget-friendly 50 watt Celestions that the stock cabs had, they just had this extra little circuit in them so you could switch from vintage,(warm), to modern, (not-so-warm) speaker cab tones.
The extra presets included in the MP-1 had a few new tones that utilized the stereo chorus and split stacks to create a wider soundscape with the guitar and a single MP-1 rig, which it does very well by the way. If you added independent delays to each channel like I did, then you started getting into pro rig territory. Add a dry center channel and you're there with all the monster guitar players of the 80's, Van Halen, Vai, Lukather, Huff, etc. Instant Wet/Dry/Wet rig. V2.01 added a few more tones but mostly with the stereo chorus for further stereo rig tones.
As for Nuno, I do recall his rig used a Boss Tuner, Distortion, and EQ pedal on the floor in front of him. I'm not sure about the distortion pedal though. I think it was the Boss SD-1 Overdrive, or maybe SD-2. It was definitely the yellow one, and not the DS-1 distortion.