With the bridge pickup, I always start out at about 5/64" (2mm) from the fretted string and adjust to taste from there. The SuperD is pretty powerful, so you don't want to get it too close to the strings. With the PAF in the neck, I would start at 5/64ths on the treble side but set the bass side a bit further down at 8/64ths (3mm). You can also play with the pole pieces heights. Having them down flush with the pickup top often creates a firmer/harder/more present tone, where raising them up out of the bobbin creates a softer/rounder/airier tone. Playing around with the heights can really have a huge impact on the balance of tone the guitar has.