#1
Hello, a while back I purchased a used Fender JagStang where the previous owner swapped in a Seymour Duncan JB model Humbucker pickup. It has never worked, and I never really used the guitar enough to be bothered by it.

Now I want to fix it, and upon pulling off the pickguard, it looks like two of the 5 wires are not wired to anything on the pickup. Is this normal? Unfortunately the only diagram I can find online for this guitar is with the stock humbucker that only has two wires.
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#2
Look for generic wiring diagrams, 99% of the time they're not guitar-specific. Sites like Duncan and Guitarelectronics have dozens and dozens of wiring diagrams listed by the number and type of pickups and controls (selectors, volume/tone knobs, etc). You'll find something close enough for your purposes there.

The white and red wires (on Duncans) are usually wired to each other and not attached to anything else. The pickguard, on the other hand, should not have any wires just flapping in the breeze. There's no point in that.
#3
with two wire pickups the bare wire is always ground , same rule applies with any 5 wire pickup. The only time this rule doesn't apply is single conductor wire like on say the seymour duncan 59 with the nickle braided wire.

For nickle braided wire it looks like this link below , or google it in general
the metal part is ground the inner wire is hot lead


for wiring diagrams
guitarelectronics.com is one site to recommend
seymourduncan has a wiring generator I suggested they make like a year or two ago too
if your pickup has two wires and you've googled a diagram ignore the north finish and south finish (red/white on seymour duncan pickups, or black/white on dimarzio)

but remember pickups have color codes for a reason if you ever do another pickup swap. With the other 3 wires you can do a lot of different stuff.
#4
Red & White should be soldered together and taped. Green and bare to ground, and black is hot. You will find many diagrams on the Duncan site, and really helpful wiring gurus on the Duncan forum as well.
Dave @ Seymour Duncan