I've recently set up my bass with the help of this youtube video:
I'm really happy with it but one question remains. Fender recommends 2mm space between the underside of the string and the polepiece for the treble- and 2.8mm space for the bass side for J- and P-basses. I can get real close to that adjusting the P-pickup of my Yamaha PJ-bass but adjusting the J-pickup is more difficult because of it's bar-shape. So I'm spot on with the E- and G-strings but the A- and D-strings are too far from the polepieces. That's because I have adjusted the action before so that the undersides of the strings are a certain distance from the 12th fret
(E->3.5mm/A->3mm/D->2.5mm/G->2mm). This results in the A- and D-strings sitting higher at the action than the E- and G-strings. This means I can never be spot-on with my pickup height for the J-pickup because if I raise it some more to be closer to the inner strings I'm too close to the outer strings.
Do I need to loosen the truss rod and reajust the action before taking a look at the pickup height again?