I took the neck off my fender stratocaster and when i put it back on it seems like the action is lower to fret the notes.

what probably happened?

should i adjust the truss rod or the bridge action?

where do i get a allen wrench small enough to adjust the individual bridge heights?
what are the average string heights above the pickups


how high should the pickups be in relation to both the strings and the pickguard?

my middle pickup is a reverse wound and my tone knobs control my bridge and rythm pickups so is my guitar a hss?
Before going on to the other questions, tune the strings like you would normally do. Now, let the guitar sit over night and check the tuning again in the morning. You'll probably have to tune it in again and let it sit for a little while. Partially because new strings stretch some, but also, because the strings are putting tension back on the neck causing it to bow back to, hopefully, where it was before you removed the neck. Now, if you changed to a lighter gauge string from what you were using, then you may need to reset the neck relief. If the neck does not go back to where it was after tuning and sitting for a while, then you will definitely have to reset the neck relief. You adjust the truss rod to set neck relief. Provided you didn't screw with the nut(which I'm assuming you didn't), then adjusting the neck relief is where you'll start. Either do a search here, or google "guitar setup." There's tons of info on how to do it.
So.... the strings aren't tightened and you are wondering why the action is messed up? roflcopter awaaayyyyy!
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