I can't help you with the wiring, I'm afraid, but as a general rule you should get as much of the harness as you can get away with.
On the wind noise, shims probably aren't what you need. The shims will determine how the door lines up horizontally (sag), when it's open, as well as fore-aft position. Adjusting the hinges to the door with the bolts will determine the height at the front and the in-out position. Once latched, the latch itself determines height and depth at the back, thus how it lines up closed. The default is one shim per hinge. If your hinges are worn so much that the latch doesn't hit the latch post on the jamb unless you lift the door, and new pins don't help, you can get some relief by taking the shim out of the top and putting it in the bottom, but since they also determine fore-aft position, if you mess too much with the shims, you'll mess up the alignment of the front edge with the fender, and might also get the fore-aft alignment of the latch too far off. However, when you get your new doors, try to bag the shims while you're there, just in case. Try to get the latch posts from the door jambs too, which may have changed a bit between 90 and 96, and may at least be less worn.
For the wind noise, your problem is more likely to be solved by moving the doors in and out at the hinge, and getting the latch stud adjusted just right. There's a lot of latitude in the door-to-hinge position, and it will take some experimenting to get it tight enough and not too tight. Some wooden wedges can help in setting the height at the hinge. Most of your wind noise is likely at the upper leading edge of the door, so the goal is to move the top edge in far enough. New doors, if they're good, may solve some of the problem by themselves, because one cause of wind noise may be just that the old doors have begun to bend outward at the top. It's not uncommon, because the window frames aren't that strong. The solution there is simply to bend them inward a little bit by brute force. Depending on circumstances that can be as simple as bracing yourself against a partly opened door and yanking on the top, or getting a robust piece of wood like a 2x4, sticking it through the open window, and using it as a lever to push the top in. This should of course be done in tiny increments so you don't end up having to bend it out again, and only if your best efforts to adjust the whole door have fallen short.
