So I found it easiest to cut unneeded connectors off of the donor harness as your pulling it.While your pulling the body harness cut the connectors off for the horn,AC,headlights,wipers, all the wires to the instrument cluster,and anything further back than the doors, as well as the relay box(you will only need 2 relays and they are under the dash).The 2 relays you will need are silver cylinders, The ignition relay has a brown connector and the fuel pump relay has a green relay.Any wires that go to either of them leave them long and ignore them.
Then lay out the harness as it was installed in the car.You are gonna need a fairly large area that the harness wont be disturbed for a couple of days.
remove all the tape and wire looms.
Pick any cut wire and trace it back to its source.Many wires will end at a splice,cut the wire at the splice but leave the splice intact until its not needed.Some wires will end at the relays/ECM.Its OK leave them long and ignore them for the time being.At the end look up the ecu wire diagram to see what wires you cut are needed.Some will need power...Its a good idea to label the various cut wires (VSS,12+ switched,etc)
As your going along the alternator harness will fall out of the harness.Set it aside for latter.Eventually it will need to be wired into the car.There are some diodes in the harness they are important-they are little brown/black boxes with 1 wire in/out.
Some 2-4 wire connectors will end up with only one wire going to them.They can cut the same as the rest of the wires.They are probably grounds for components that don't exist anymore.
After you have ran out of cut wires I like to cut out the HUGE body connector and splice the wires because it saves space.ONLY cut/splice ONE WIRE AT A TIME!
I like to collect and group up various leads by function ie all wires that need 12V switched power,or 12V in run,etc
Tape the stripped harness every couple of inches and test fit it in the car, you may have shorten/lengthen varius wires to get the harness to fit how you want it to.Remove harness to modify harness,then test fit.When your happy with the harness remove from the car for final taping/wire looms.