Re: JB vs Custom vs Custom 5
It's not a question of "sounds better" -- not when you're comparing quality pups. It's more of a matter of "given this context, which pup will give me this or that sort of response?" What are you aiming for with your current setup? It's usually better to adjust what you already have, than to buy a whole new pup.
Now for something directly/immediately useful. You can't go wrong with any of the Custom pups -- not only is each one built to sound great in a variety of situations, but each can be converted into any of the others with great ease and speed merely by changing the magnet. The Custom 5 is like a beefed-up PAF, with great cleans, and the plain 'ole Custom is basically a pissed-off PAF, with more modern cleans.
Now for the fun stuff! As I said, you can swap out the magnets to convert any Custom into any other Custom. It's cheap and easy, and a lot of fun if you're a tinkerer. I suggest going to forum bro wymoreguitars.com and ordering a few humbucker mags; use the coupon code sdforum for a nice discount (thanks, Wymore!). Get an Alnico 2 and an Alnico 8 to try in your JB while you're there; a lot of people have been happy with their JBs after doing so.
Myself, I started with a Custom Custom in the bridge and a Jazz neck in a PRS SE (basically an SG) In very specialized circumstances it sounded great, but sub-par otherwise. I'm now using a C5 with a slightly degaussed magnet and Jazz 4. Degaussing A5 evens out the response a bit (full-strength A5 is heavy on the top and bottom, light on the mids), making it closer to A4. A4 is a bit stiff, without the chimy overtones of A5 or the lush overtones of A2, but it sounds great in a Jazz N -- tonal Viagra. I'd imagine that a degaussed '59 would sound even better, but not $60 better.
Yeesh, sorry to ramble and rave. Gotta be the flu and the meds.