About a month ago i bought a Seymour Duncan JB Jr for the bridge position in my Squier SE Strat (lowest quality from squier i believe) but it sounds very nasally (i believe it's out of phase) and the neck pickup has no output (it's basically a killswitch), would taking the strat to get rewired to be in-phase improve the sound?
head over to the wiring thread and I'll help you out further, but include a diagram of how you wired it as well.
also, does the humbucker sound nasally and thin when you use it on its own, or only combined with the other pickups? and does the output level drop when you go to the out of phase sound?

as for the neck, did you disconnect any of the wires or anything? did you re-wire it yourself?