i've messed about with pup height, im yet to try the guitar through another amp, but the amp im using should in theory have all the gain i want, since its supposed to be designed for metal, it sounds great through my maverick f1, which has passive pickups. i mean the harmonics are there when i play, but there just doesn't seem to be enough strength in the sound to make em really stand out. the ML was designed to use the shape of its body for high sustain and resonance right? maybe it was just never ment to house EMGs?
but again, with or without the harmonics, the EMG's are pretty stale sounding and i know exactly what you mean when you say there one dimensional, ive heard there sound being described as sterile. i think thats the best way of describing them!