Passion And Warfare era was played using:
Ibanez Jem with DiMarzio Evolution humbuckers (some more recent tracks like "Bad Horsie" used DiMarzio Breeds)
Boss Distortion pedal (probably a different distortion pedal to what he uses now)
Morley wah pedal (now tweaked and remarketed as the Bad Horsie)
Eventide Harmonizer H3000 digital effects rack effects (not sure if it was the SX or the D/SE)
then a bunch of cabs (now mostly Carvin gear).
The tone he achieved for all of his effects was done on an Eventide Harmonizer (now discontinued) - you can still pick them up on E-Bay with the Vai patches intact (I got one a while back - excellent piece of gear but quite expensive)...
As far as using a GNX series goes, you can get an approximation on the Digitech forum... it may be close but it won't be the 'real' thing.