I find that I can control the squeal pretty easily and the tradeoff in better tone is worth it to me even if I have to lower the gain. Come to think of it, when I am playing at full band volume I use about 1/3 to 1/2 less gain than I do at lower volume so that is already taking care of a lot of the problems.
I don't know the measurement of the Legacy pickups, I adjust the heights by ear, but the neck one is easily 1/4" lower than the strings when fretted around the 15th/16th fret. The middle not much higher and the bridge not much higher than that. I don't like Strat/Legacy pickups very close to the strings since the polepieces are actually the magnets and the tone gets too compressed for my taste.
Of course, you know me and my OCD/ASD annoyance with any kind of noise or squeal...but I can appreciate your description. I want to be able to stand in front of a cranked amp without squeal, and I can finally do that with the GFS PAF clones. Both my Gibson 57 classics and both sets of Gibson 490's buzzed and hummed like a Fender single coil, even after shielding and the Tone Man Vintage Wire Harness.
I couldn't stand it...








