i would go air norton(neck) and tone zone(bridge). that is what i am going to put into my new RGT3120(actually an air norton and air zone). petrucci used both these pickups at different times. for day and dream and images and words, he used the humbucker from hell and the tone zone, from awake to his deal with EB/MM, he had the air norton and steve's special. i personally have used them all except the steve's special, but i personally love the tone zone. i also love petrucci's clean tones and
neck pickup tones in his lead work and have played on an air norton before i ever bought one. to me it is near perfect. the humbucker from hell is what it claims to be:a single coil sound in a humbucker space. i had it stock in a pgm500 and it was very very single coil voiced. i liked it for a single coil sound, but i have strat's for that. the air norton is fat, but if you want sometinh not as fat and agressive as the air norton, the fred is a great pickup, too. right between where your stock
paf pro and air norton are. i have a fred in an rg550 and an evolution in the bridge. both complement each other amazingly well. the fred is not as fat as the air norton, but has a nice mid range attack for "cleaner" sweeps and clarity. the norton is a tad muddier, but i like the balls of it better. plus the air norton is smoother. both are really good at dynamics and are really expressive with different types of pick attack. personally, though, i would just wait and get the axe, play it, then decide if you really want to swap pickups.
rich