I'm slowly finding it hard to make any mods to any of the models since I get along with them as/is. Out of all my favorite mods, they would have to be Kurt's pickup swaps, and the Mustang with the Univox control panel and pickup, soundgarden sticker, and record for a pickguard, that thing just had character. I almost want to build a replica of it.
The EMGs in my Jag Stang were not installed by me or even my doing, I wanted to do it beforehand, but the previous owner of that guitar did it, and I bought it that way because that was just PERFECT for me. Add a treble bleed and wire one switch as a pickup selector and I've got all the versatility I need for most things that I usually do. Same deal with the Cool Rails, except with those I originally planned to swap those and put a black pickguard and pickup covers on the guitar, only to decide it was not work the money just to have the same sound with a different look, so I decided to make the guitar it's own sort of entity by using the cut-off pickup cover mod I saw on here with the claw installed.
On Japanese Fenders though, I do change some things on the bridge quite a bit. Shorter screw on the low E saddle, tighter springs on the E's of Jaguars and Jazzmasters, and 3M tape on the bridge action adjustment screws to keep them in the right spot.
One Idea on the Jaguar I've had for awhile is recessing that Vibramute, I like using it, but I hate how I have to shim the neck, and raise the action to use one. So I might adopt a bit from the Floyd Rose recessed trems, and recess one into the body of another CIJ (preferably one that's already bastardized as a partial Restoration project).