Hey MJMP, this is where going to a parallel PU switching can help, you may not need to add as much presence boost, but hey dial it in if it works/needs it. I've also stared to lower PU height (you don't need much to make a difference), and you can use a vol pedal (IIRC you do ?) before the preamp to back off the input if you don't want to roll vols down. So on JPLP for example, I get great tones with PUs on 2.5 to 3 /10. And you have all the voices between 1 and 5 to play with, maybe try voices 2, 3 & 4 with PUs backed off (allot). I started playing around with one of my MP2s to get good sounds for my Epiphone SG the other day. It has 57 gibson re-issues in it (so not super high gain PUs but great sound/character) and was kind of on a similar journey to what you are wanting I think. I got some tones I didn't mind and I started looking into the other MP2 voices which I've never used (basically I've only used 1, 5 and 9 or 10), also it's always been with the Anderson and Ultrasonic PUs, time for new blood. If I come up with anything decent I'll let you know (early days but good results so far).
Wow, interesting re the Classic, I thought it was a transition to the MP2 but it makes sense that it was like MP1 with some MP2 features. And also that some found the MP2 too complex or didn't like it. I must say I've never spent the time dialing in tones in the MP2 which I did with the MP1. I just grabbed Big Fat Crunch or whatever, tweaked it a little and went for it (I had gigs to do..). I solved the clean sound by PU switching/combination.
Now MJMP I'm assuming you want to be able a get a good clean sound from your EMG guitars and then switch back to high gain sounds ?. The EMGs should be able to cope, they started life as great clean PUs (not that I've kept up with their development), and rolling back volume pots is more stuff to do in a quick transition (hence vol pedal suggestion). Split col PU switching is another option, again it's backing off the input but also changing the PU impedance (though as EMGs are active
). By and large great clean sounds tend to be single coil PUs, humbuckers switched in series tend to muddy the waters but depends on the tone you want.