I recently purchased a Jackson SL1 USA soloist, brand new never used back in Jan 2012. I have been struggling with the set up ( especially on the higher strings above the 12th fret, and the G string always seems to sound out of tune. I'm tuned to standard down 1/2 step and Im using a custom gauge Ernie Ball strings set (low to high 52 42 30 16 11 9). I have done multiple truss rod and intonation adjustments and still cannot find the sweet spot. This particular set up works great on my les paul and other guitars, but doesn't seem to mesh with this Jackson. Any tips or advice on which string gauges to try or what I might be doing wrong is greatly appreciated, Thanks

String Height:
Low E @ 12th fret 5/64
HIgh E @ 12th fret 4/64
(any lower string height causes excess buzzing and out of tune sounding notes/chords)

If you purchased it used (you did not say in your post) it may be in need of a fret level and crown.. If you have not set up a Jackson before, remember the fingerboard is not flat, it has a radius.... It may also be in need of a truss rod adjustment..

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Chaos, panic, and disorder.. My work is done here.

Disregard my original post, I was just being dumb and wasn't tightening the truss rod enough. The truss rod adjustment was so stiff that I thought it was fully tightened, but it actually wasn't. Glad I figured it out before I mad an ass of myself at a repair shop. So I went back and set it up in Eb with 10 -52 strings and it plays pretty good.