#1
So I upped the string gauge on my Ibanez S-series from 9 to 10, and of course the intonation and action both became completely off. I managed to fix the action pretty well but can't adjust the intonation any more...(in tune on open string, drops a little under a quarter step at the 12th fret and a little under a half step at the 22nd).

The saddles are as forward as they can be so I'm not sure what else I can do for the intonation.

Anyone got any suggestions?
If you think things can't get worse it's probably only because you lack sufficient imagination.
#2
did you adjust the spring tension?

if your brigde is being pulled foward your intonation will be off.

it sounds like your bridge was being pulled forward and up, so insted of adjusting the spring tension you adjusted the bridge height. is this correct?
Guitars:
LTD Alexi-600 White & Black
LTD Alexi-200 Black(Death Adder pickup & Gold OFR)
Agile Interceptor Pro 727 7-string
Jackson JS30RR rhoads
Jackson DKMGT
Squire telecaster

amps:
Bugera 6262 212 loaded with WGS veteran 30's
#3
I took care of that, I made sure the bridge was parallel to the body.
If you think things can't get worse it's probably only because you lack sufficient imagination.