The good news is you have “one of the best distortion sounds you heard” so I would mark that and keep it right there.
As for tonal differences between amps and pickups there are always going to be huge differences so the only way to test that out is to try another guitar and amp. You may also want to change pedal order etc.
If you are concerned there is a build issue you could recheck all caps and resistors by color band especially around that stage of the circuit (nobody is immune to a mistake) then re-flow the project and verify with an Audio Probe. I can’t make any guesses beyond that. This was not my experience with a Les Paul w/ PAF pickups into a Marshall.
It begs repeating if you are getting a great distortion with the settings available it doesn’t matter where they are on the dial since they are there to accommodate different rigs and ears.