Here's my current favorite mis-matched combo in a semi-storied guitar:
C-Bomb Bridge (Green), PK Neck (Pink) in an Ibanez JEM77FP (early 90's model). This is a phenomenal combination in this guitar. I wanted to improve on the tone of the instrument and not stray too far away from the Vai-like sound I could pull out of that instrument. I started with the C-Bomb bridge. It just roars and cries from this alder guitar. I've tried it on multiple amps in guitar shops and it has a massive, dark and focused sound to it without tremendous compression. The PK neck compliments the C-Bomb perfectly. I wanted a powerful, fat, and ceramic compressed neck sound for very aggressive leads. The EVOs were just flat and you really had to dig into the instrument to get them to sing plus they were very muddy. The C-Bomb/PK combo makes notes just fly off the fretboard. If I roll the volume back slightly they clean up beautifully (Die To Live tone). That's another point: this combo is very controllable. If I want softer, more open and fluid like clean tone from the neck all I do is roll the tone nob back slightly, about 7/10, and lower the amp master volume on the clean setting. The spikey, ice-pick shrill that sometimes comes out of the PK neck are non existant and on clean it warms the sound up making it less glassy but still clear. I recommend this combo for any super-strat. It nails the modern Vai tone but has more power and plenty of its own character, as well as being metal as $%. In fact it's a better modern shred/metal combo than anything but it does have refined dynamics and is capable of a lot of rock/metal tones in a variety of tunings. This combo has way more balls and snarl than the EVOs or Original PAFs had.
This axe used to be owned by Steve Vai as a soundcheck instrument before it wound up hanging in the window of a music store not far from his parents house, collecting dust. I stole it (off of ebay) and the previous owner provided some good paperwork to back up the story. When I got it appraised (for kicks) the G-Center manager was horrified I was going to change the stock pickups and ruin the original sodering. Well, the store owner from NY said it was a really a players instrument, showed road wear, and definitely was begging to be played. I couldn't agree more. The recent upgrade to BKPs gave new life into this instrument, and I'd love to hear that G-Center Manager's opinion now on whether or not it was a good move to "devalue" this collectable. You don't tune up a classic to not drive it. This tune up was like adding a brand new twin turbo engine, straight piped. I can't recommend this combo enough!