For the Cleans, use the MP1 Solid State Clean, Bass -2, Mid -4/-6, Treb +2/+4, Pres 0. Dial in some Compressor (OD2 in S.S. acts as compressor)
Add a nice shimmering Chorus (Intellifex 8-Voice) and some Delay (200-300ms, 2-3 repeats).
JP also normally uses a Phaser or Flanger before the (Pre-)Amp on his Cleans. ADToE Album Cleans are a combination of Piezo and Electr. Guitar Cleans......but the above settings should get you in the ballpark.
Crunch/Main Rhythm: Tube Dist. OD1 6, OD2 8, Bass -2, Treb +2/+4, Mid -2/0, Pres -8/-10
Add some Chorus (20% wet/mix) and a 7ms delay
Lead: Tube Dist. OD1 6, OD2 10, Bass -2, Treb +2/+4, Mid -2/0/+2, Pres -8/-10
Add same Chorus as Crunch/Main Rhythm, Stereo Delay 250R/500L, 3repeats (for faster Leads); 400L/800R, 3repeats (for slower melodic Leads)
If you have, put an EQ (5band graph/parametric) in the Loop BEFORE the FX...theres some pics on the web of JPs EQ settings, basically the V-Shape and another half-V kinda with the 2200 Slider a tad bit higher and the 6600 Slider around 0/+2
(
Triaxis Manual, page 10, bottom 2 EQ graphics)
Hope this helps for starters.....
BTW, what guitar/pups are u using??
@El-C: Anything wrong with being a JP fan???
Sidenote: The squeal you mentioned could have its cause in/at the front pot