If you go with the 3 Wire (more preferred) Here is a diagram for that, you say it's 3 wire now, but as I understand it you will be going to a new engine harness, with options..
This is 3 wire internal:
Simple and easy to hook up, Run one 10 gauge red wire from the main (large lug) Bolt on the Alternator to the area of the starter solenoid battery main bolt.
On that wire, Install a properly gauged fuse link . If your new Alternator is 80 amps go 85 or 90 on the link.Hook it to the main battery terminal on the starter solenoid.
The second wire, will be a red 12 to 14 gauge wire to any voltage source, switched (I find is better) but "Hot at all times" is how the factory did it..Either way is fine!
Next run an 18 Gauge Brown/White wire from the #2 terminal, to the "Hot in Run" Side of the ignition.
If you have a Charge light, Run an 18 Gauge Brown to one side of the indicator, Exit that with a Pink 18 gauge wire into a fuse/Fuse holder, into a pink/black 18 gauge wire to the "Hot in Run" side of the ignition.
Unless you have an 81 Alternator, disregard the 3 rd red wire, not used.
INSTALLING CONNECTORS THAT WILL LAST:
Do NOT just use Crimp on Connectors, Use a proper size uninsulated ring and, IF needed , uninsulated, Solder-able Butt splices.
To do the job right, Strip the wire to the proper length, about 1/8 on an inch extending out the terminal, no bare wire to the rear. Tin the wire with 50/50 solder. Then slide 2 each, about 2 inch heat shrink tubing over the wire and go to the terminal.
Next tin the Terminal wire "Barrel" (where the wire goes through) until good and smooth and shiny. Then slide your wire into the ring, make sure you have no uninsulated wire hanging out the back.. AND no wire into the ring hole, trim if needed!
Crimp it firmly. Next, solder it, adding a small amount of solder as you heat it, until you get a smooth shiny connection..
(Grayish or dull is a cold joint, reheat, and add a tiny bit of solder until you get the above results.)
Let it cool, then slide the first piece of shrink tubing over the ring and wire, hold or prop the wire STRAIGHT and shrink with a heat gun.
(If you have like for days..a hot hair dryer will work, but take tons of time..Don't use a lighter, or solder gun..this just melts the tubing and possibly the wire below it.)
Next, slide the second piece of tubing over the first, but offset it by about a 1/4 of an inch, holding it straight out (if it won't stand straight on it's own by now ) Shrink it down also. Let it all Cool down, and move on!
This will not only provide insulation at the terminal, but some amount of wire strain relief, and It looks REAL pro done if you do it right. BE SURE to make your tubing end cuts straight..(HINT: use a paper cutter, with an adjustable fence.)
On the Butt Splices (If you must use them) Use a proper gauged splice, Metallic, (no insulation) Look at the splice, you will note an inspection hole that goes to both sides of the splice..
Strip, prep, and tin your wire as you would for ring terminals.
Slide your wire into the splice end (trim if needed so some insulation fits in there) Crimp the one side. Do the same on the other, but before you commit yourself, slide two lengths of shrink tubing over the wire, the first to be about 1/8 inch longer than the whole splice, the next slightly longer, about a 1/2 inch..
Crimp, then find the inspection hole, using a vise or something to hold the wire, Heat the Metal Splice and feed a small amount of solder in the inspection hole..continue to do so until it has filled it in.
Then Slide the LONGER shrink tubing over it and shrink it down, Next slide the shorter one over that and shrink down. This will give you good insulation, and anti chafe, Plus with the inset ends looks again real pro done!
Use this method For all smaller gauge wires (10 Gauge and down) and you will have a system that will last forever, and look good while doing it!
Larger gauge wires (Battery Cable, Frame to body cables, ground cables) Require a Nicopress to install the crimp ends..Don't solder them It will just heat and drip out the ends..Don't try crushing them in a vise..usually the first time it is stressed the wire will just pull out..
If you don't have one ( and I suspect you don't) Have the hardware store, Electric supply, or an electrician install them, they will have the tool.
Everything you never wanted to know about harness Building 101..
Hope it helps, gives you some direction, and hopefully apply it to your new harness install as well..