I just noticed this thread's been here a while and not garnered much interest - which is a shame because I'm sure a lot of techie types here could help with answers! As ever I'll chime in with some ill-informed and badly-explained opinions in the sure and certain knowledge that someone will correct me.
Anyway what's vintage wire stuff do? I'd randomly guess it would be something to do with treble roll off.
It conducts electricity, just like modern wire. The main difference is the cloth covering which some people prefer to work with. Some people may go so far as to claim it sounds different - clearly these people have ears as sensitive as the average radio telescope. The best argument in favour of vintage repro wire is that it looks cool and "aged" and "roadworn" (ugh).
If you swap round the hot and ground (south start) wires on a pickup I believe it reverses the phase, so does anything happen to the tone if you reverse phase all the pickups in a guitar?
This is a more complicated question and quite tricky to explain but I'll have a try.
Pickups generate Alternating Current (AC). This means that as the string vibrates up and down in the magnetic field, a voltage is induced in the coils of wire. But this isn't a steady voltage like you'd get from a battery, the voltage goes up and down at the same frequency that the string vibrates.
Stick with me, I'm getting to the point slowly.
If your pickups (let's say neck and bridge) are in phase then the voltages from both pickups will swing up and down together. This means that the voltages add up, re-enforcing each other.
BUT if one pickup is out of phase (hot and ground wires swapped) then the voltages partially cancel each other out as one pickup will produce a rising voltage as the other produces a falling voltage. Long story cut short, some of the frequencies cancel each other out, you get a thinner sound and less output.
EDIT: to answer the question - if they're all "out of phase" then really they're all in the same phase - so the voltages from each pickup aren't cancelling each other and you will
theoretically get the same sound as when all the pickups are in "normal" phase. What you'd be doing is turning all the voltages upside down so they'd still be re-enforcing each other. It would probably sound a little bit different from normal but I'm not about to pull a load of wires out of my guitar to find out.
EDIT EDIT: to further confuse you, there are two ways in which a humbucker can be out of phase. Its overall output can be out of phase with the other pickups and/or the two coils of a single humbucker can be in or out of phase with each other.
What's the bare wire from a pickup for if there is a already ground? Seems to look like another ground wire but then why would you need 2 grounds?
Adding a grounded metal shield around a low-signal cable protects it from stray interference. It's also necessary to ground things like metal covers to reduce buzz from capacitance effects caused when you touch the covers.
Output jacks only go to ground through the strings right, they can't go to ground through the instrument cable through the amp?
Everything on the guitar is grounded to the output jack (or the bridge) and the output jack ground is electrically the same as the amp ground. The strings are grounded for the same reason as the pickup covers.
I'm hoping JPF or HTH will give a more technically informed rewrite of this!