HUGE update here.
The resistors I had changed really had
nothing to do with my "problem".
I'll explain...
I originally had my MP-2 rack set up as I normally would always have my previous MP-1 racks set up.
Everything in Series: MP-1 > FX unit > poweramp. The poweramp Level stays about 75-100% and I'd control the overall level with the FX unit's Output Level. Once the preamp patches, fx patches, and everything's all dialed in this worked great. So I automatically wired up my MP-2 rack the same way when I got it with no problems. Later on, I changed the routing to put the FX unit in the Loop (something I would never, ever do with the MP-1) because I figured this way I now had options. I could now take advantage of the MP-2's pretty darn nice Recording Outs if I ever needed or wanted to, and the FX would appear in those Outs. If I would happen to use the Recording Outs in the old version "Series" routing, no FX would be present in those Outs, just preamp...which might be fine if I were to do some kind of W/D/W setup but I'm not interested in doing any of that.
So that "problem". I was still using the FX unit's Output Level to control overall level, and when I needed to turn it up a bit,
I was overdriving the Loop and causing all kinds of bad artifacts to pop up and generally just blowing everything past the Gate.
It wasn't always apparent with the Clip LEDs, but that's what was happening because turning the FX Output Level back down cleared it all up. I could've kicked myself. So I went through and re-optimized all the levels across my presets and patches and now my overall level is controlled by the MP-2 Output Level, as I always should've done in the first place.
Case Closed, and everything is back to fine.
And by "fine" I mean raining doom, despair, fire and destruction down among the forlorn, the downtrodden, the tired and forgotten.