I have Texas Specials on my strat, and I really like them. One thing I've noticed about them since I've gotten them on (I used to have '57/'62's) is that the G, D, and A strings sound out of tune when played, even though the pitch is right... if that makes any sense...

I noticed that on those 3 strings, the magnet poles are much higher than the others (especially on the G string where I notic it the most). When I play notes, especially ones higher up on the neck, it seems like the magnets pull the note out of phase or out of tune. It also greatly decreases the sustain.

Are my pickups to high or is this just something I'll have to live with?
Lower them pickups! If that doesn't fix it, something else is to blame.
Quote by ratmblink123
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Your pickups are too high.

Lower them incrementally and by very little each time to get the right balance between tone and functionality. Also, it sounds like you only need to lower them on the treble side really, but make sure each string sounds balanced at the end of it all.
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It could be your inntonation, play a harmonic on the 12th fret, then play the fretted note on the 12th, if they sound different, it's your inntonation
Dissonance is Bliss

Signal Chain:
Carvin CT-4
Ibanez TS-9
Carvin Quad-X
TC Electronics G-Major
Mesa/Boogie 2:90
Ear Candy BuzzBomb

Member #4 of the Carvin Club
I'd suggest lowering them. I started a the "recommended" height for them. Had a harsh, muddy mess that didn't sound right for anything. At present, I have them about 3/16" above the pickguard and they sound pretty damn nice.
My Gear:
Gibson Les Paul Vintage Mahogany
1993 US Peavey Predator with Texas Specials
Crate Palomino V16
Boss OD-3