Mind you, drunken post...
The first rule of order for anything in my flock with a Fender Dynamic Trem is this
viewtopic.php?f=1&t=14552&hilit=+whammy
On a Jag-Stang, I'll usually swap out the pickups with something else, pretty much anything else, could be a Schaller S6 and a DiMarzio Super II, an EMG SA-1 and EMG 81, a Seymour Duncan Vintage Flat and a Seymour Duncan JB, a Seymour DUncan little screamin' demon in the neck and a Seymour Duncan Screamin Demo in the bridge....whatever. Could be something as odd as a P-90 in the neck and a Bill Lawrence XL-500 in the bridge. I'm not terribly picky as long as it sounds good.
Wiring is then redone depending on weather the pickups are active or not, active pickups are wired like my current one, passive pickups are wired like my Mustang with a coil split in the bridge (no need of redaundant phase reversal on both pickups).
And that's pretty much it save for any cosmetic changes I would make to make it stand out amongst my other guitars.