Hey Tommy,
If the MP-1 was having issues before you installed the mods, then more than likely, the issue is still there. It was never addressed before you installed the mods, so it still goes on even with your hard work. I wished I had known that before you went to all the trouble you did to install these mods.
Even a stock MP-1 operating like it was originally meant to does not sound thin in any way, unless you dial it in that way, and you pretty much have to turn everything almost all the way down to get it like that. It's a robust and full-bodied preamp that was powerful enough to turn the entire amplifier industry on it's ear when it was introduced in 1987. (As was evident in 1988 when all the other single space rack preamps began to show up on the market).
There is something in the un-modded circuitry that is already goofy with that preamp. Perhaps you might be able to get MJMP to help walk you through some checks with that preamp to try to figure out what it might be. I'm pretty sure this issue has come up in the past with stock MP-1's and it's been addressed here on the Forum. You might be able to find it in some old posts, but I would run this by MJMP regardless, and let him point you in what might be the best direction to figure this out. The only thing I can say at this point, is that you have already narrowed it down to an issue with the tube voicings, since you said the SS voicing sounded very good, that takes that part of it out of the equation. That also means the issue is common to both clean and distortion tube voices, if they sounded thin before the mods. I don't know this for a fact, but I'm going to guess that it's somewhere in the power to the tubes circuit. I would start with a meter on the tube filament voltage to see if you've brought it up with the transformer mod. The stock MP-1 ran the tube filaments at a lower voltage to begin with, around 6.3 volts if I recall correctly. So I would check the filament voltages at all 3 tubes, and also, check your grounds to both circuitry and chassis for cold or incomplete solder joints. Weak tubes sound like dogshit on razor blades. I would also check the output voltages at the transformer to be sure it's not damaged in any way.
Harley