I would disagree with Bartamos on one point: question 3.
It can be very helpful to have the existing wiring in place while you are figuring out the routing for the new harness. All of the existing wiring should come out, but not necessarily "first".
And definitely don't cut off the "extra" wires. Make sure the ends are covered so they can't short against anything and/or remove the fuses powering them and zip tie them out of the way for the eventuality that you want them in the future. You don't want to discover 3/4 of the way through your project that you cut off a wire you needed and have to put it back.
For sealing the ends of wires, I like to fold the end over into a J and put a pieceof heat shrink over it to fully cover the end. I find the heat shrink is less likely to accidently get pulled off that way than if I just put it over the end of the wire.
