Re: Replacement pickups for CIJ Jazzmaster
The stock pickups on a CIJ are the best. And with the added switch on the upper horn, and 2 different tone knobs, you'll be able to dial in whatevber jazz tone you need. The only thing you need to do to a CIJ jazzmaster is install graphtech saddles, because the strings always come out of the stock ones, and on mine, the action would lower itself on every strum. I tried the SD vintage set on my jazzmaster, it made it sound like a lespaul with the tone down, complete garbage, I put the stock pickups back in, and its the perfect guitar.
...the issue with the CIJ pickups isn't that they're bad, theyr'e just not constructed like traditional Jazzy pickups

If you like strat pickups better, you'll probably like the CIJs. Jazzy pickups are mellower, hence the Les Paul vibe you were getting... I slightly prefer Jags to Jazzes for this reason, Jags are brighter (but they can also be just as mellow as a Jazz)
But yes, Jags/Jazzes are probably the most versatile guitars in the world

But you actually use it for Jazz? Good stuff
...As for your bridge issues, don't get me started :laugh2:
You don't need graphtech saddles, you just need a file to deepen the grooves... But before you even do that, if your saddles are lowering themselves, you need to lock them in place... basically, put the saddles all the way up (which stops any rattling too) and adjust the bridge posts down so that there's just a millimeter or two between the baseplate and the body... just enough that it can rock. (this method also means the bridge is more stable in general... can't get pushed around)
(You MAY need to remove an unnecessary neck shim to get a proper setup on some Jags/Jazzes)
The only other mod I'd recommend on an MIJ/CIJ Jazz is to check the trem arm... some of them are cut too long and bottom out, not giving you as much range as you ought to get.