MJMP,
That is correct, the Classic came after the MP-2, and was intended to be an upgraded version of the MP-1 with a stereo effects loop, built-in noise reduction, and dedicated recording outputs. It was never intended to be anything close to the MP-2 since that was very unpopular with guitar players, it was too program intensive.
I never used EMG active pickups, so I'm not familiar with them. They don't clean up? Have you ever tried getting a good clean tone just plugging into your Marshall? If so, what happens?
I used to play that song. Mark Kendall was playing through Randall amps back then. I nailed that tone with my G-K when I was playing it, (didn't have the MP-1 yet). I will get down to my studio this weekend and try to work that tone out on my Classic this weekend, but I don't have any humbuckers that hit the amp as hard as those EMG's. May I suggest lowering the OD1 and adjusting the OD2 to try to clean it up a bit? When I played that song, I used my Jem guitars and those had DiMarzio Pro 151 PAF's in them, so the Flying V might be your best bet.