Bigger G-strings are kinda uncomfy, but when you get use to the perpetual wedgie that you have I'd expect you get use to it
But in all seriousness, you shouldn't have to worry about the pickup height at all. If you're happy with the tone you've got atm, just leave the pickup height the same. If the sound changes to the point that you don't like the way it sounds (too muddy), drop the pickups lower.
You shouldn't have to adjust the truss rod
, atleast I wouldn't think it would make *that* much of a difference.