i've spent long neurotic hours trying to get my G and low E strings to correct intonation.
my guitar's got this ZR2 trem.
the scale length is very out of phase and i find it impossible to shift them.
meaning, if you put your guitar vertically, the saddles look like they are ascending from low E to D, and then back down to G ascending to high E.
but my G and low E is not in order.

i agree with toker420 here, but if you don't want to spend 50 bones to get it set up, here's what you do...you'll have to drop tuning on all strings and unlock the nut (provided you have a locking nut) and continually adjust the pitch back to your tuning, and adjust the springs in the back, obviously, you'll have to push the whammy bar all the way to the body to unlock the saddle screws. The ZR2 trem has two different positions for the saddle screws. try alternating the positions to see if that helps. It takes me about a full 2 hours to set up my trem after i adjust tuning. If all else fails, if you have a bolt-on neck, you'll have to get the truss rod adjusted which you should NOT DO unless you're a liscenced professional. If you need the rod adjusted take it to get professionally set up.
zr2 doesn't need all that fuss anyway i solved the problem.
since the "out-of-phase" saddles are positioned high above the others, i

loosen the string (very loose)
loosen the saddle lock a bit
push the saddle with a sharp-tipped plier (for a longer scale length)
while maintaining the force, tighten the saddle lock
then finally redo intonation adjustments as normal

i didn't figure this out until just now and i had been stuck in cycles of adjustments in vain.