Ok... That's Eric Johnson. You're biting off more than you can chew to try to chase his tone. Seriously. That guy is THE biggest gearhead I can think of.
Anyways, I think your problem lies more with the pedals, speakers and amplification than pickups.
Single coils by nature are already low output, so they would not be as harsh as a high output humbucker, and can be controlled using various drive pedals. If you want a smooth tone for gains, then use a Boss SD-1 instead of some metal tone pedal or even a DS-1. You need smooth overdrive and not distortion. You need to play with low gain tones rather than high gain stuff, or use a low gain pedal like the SD-1 overdrive as a tone shaper and something else as a gain booster.
Clean-wise, what's wrong with your pickups? Ignore the distorted tones.