Not sure about pick guards, but I have a cousin to your bass, an '87 ish Fender Jazz Special with a 32" neck, black finish, gold hardware, and it seems that the biggest issue with refinishing is damaging the value of a bass for resale since folks seem to appreciate having an instrument in its original condition. For instruments like ours, though, being both of a newer vintage and not being worth thousands of dollars with decades of history in their dings I think it would be less of an issue.
For what it's worth, though, I'd never refinish any of my basses; I love all the dings and marks. The hardware though I would clean up just to be sure there's no rust getting into the core of the screws or load-bearing elements. Not sure what you would do for gold hardware though, chrome is so much easier to deal with.
As far as the pups are concerned, and I think my bass had almost identical electronics to yours (mine apparently was a sort of early forerunner before the P-Lytes were put into production), I put in a P/J set of Seymor Duncan Quarter Pounders and fitted them to Stellartone Tonestylers for the tone pots and just used some Noble volume and blend pots from Best Bass Gear to round out the setup.
As it is, it's freaking unbelievable. Total dark woody bass from the split P dialed in, and bright, hot bite from the J when the treble tone is punched up a bit.
This is one bass I'll never sell.
85/6 MIJ Fender Jazz Special 32" medium scale bass
