If you feel you have enough gain coming from the amp and/or pedals then the pickups is more a matter of what voicing you like. The PAF Pro is pretty cool in the bridge but it's a bit small/focused-sounding for my taste. It has the honky "notched" mids which can be good or bad depending on your preferences.
The Super Distortion is a HUGE sound, it's massive. The Super 3 is a bit more mid-focused and it has a bit less high end. Both kick ASS!
The 36th Neck is great but for metal it is a bit underpowered IMHO. It doesn't feel that great to me doing shreddy stuff, I like more compression, like the PAF Pro or Super 2.