Ah, choices. Always fun to get sorted!
Here's my opinions: First, swap out that "quirky" front panel on the #3 MP-1 that is currently impressing you the most? Make that one perfectly functional and leave the rest of it alone if there are no other issues with the unit. (Use the front panel from the MOD 3 unit)
#2 MP-1 gets your choice of 3TM or MOD4, and leave the MDRT in it for now.
#1 MP-1 needs some work. Might be a faulty Mod or Mod Install, or might be the Mod is in a faulty unit. Btw, there's an update on the MOD3 to MOD3.1 that improves the lead tones of that Mod....but if the unit is faulty to begin with then a Tone Mod won't help. Maybe return the unit to stock specs then get it sorted from there? Once it is back to good working order, mod it to whichever Mod you didn't install in #2 MP-1. Now you can swap the MDRT between the #1 and #2 MP-1 to see which one likes it better. Be prepared to make this one a "Parts Only" unit if things go sideways. I see nothing wrong with having a Parts Only MP-1 when you have two other badass MP-1s.....