I did this not to long ago with my 68 Barracuda. I knew I needed to undo my hack wiring for my pump and fans etc. I also knew I needed a better alternator to support these systems. I was also very aware I didn't want to rewire the entire cars lights etc.

I went and removed every bit of wiring that I added on. I then cut the engine part out of the under hood harness. Take note, on my 68 the horn wire was in that bulkhead connection despite the fact that it is really should be in the lighting section as that's where it runs. This caused me lots of problems when I tried to fix the horn for drag week LOL.

I relocated my battery to the trunk. I made a 12 circuit relay panel that is located in the glove box. Don't make a relay panel, it will cost less to buy one don't ask me how i know. I ran a 4 gauge wire to a power stud mounted above the kick panel on the passenger side, from this I powered my relay panel. I then took the ammeter wire and moved it to this power stud. This eliminated the bulkhead connection and powered up the factory fuse block and allowed the lights etc to all work. This was a HUGE improvement, everything works so much better and brighter with no ammeter and no bulkhead connection.

For an alternator I ended up with a GM CS130, not really by choice but because it fits the alternator bracket that goes with my mezziere pump. It also happens to be a readily available piece that is 110amps or so.

I wired the alternator up off of a diagram I found online with a charge light and ran the power wire to my power distribution point near the relay panel. I have 14+ volts at a 1000 rpm idle with everything on, lights, pumps, fans, etc.

I also put a jeep starter relay at the back of the car and ran the starter wire from the back up to the starter. The jeep solenoid works off of a ground just like the factory starter relay, this lets the neutral safety switch work like factory. This also allows that big long starter cable to only be hot when the starter button is pushed. This also cleans up the engine compartment a lot.

Now, the only problem with this setup is this. I ran the field wire from the alternator all the way back to the cutoff switch on the car. The cutoff switch has two sets of poles one for the alternator and one for the power wires. Somewhere I have wired it wrong and it doesn't shut the car off. I believe I need to bring the hot wire from the alternator to the battery side of the cutoff switch.

Summary, lights all work just like factory, wipers as well. Everything else that makes the car run is powered from my relay panel that is switched off of my center console. I also have a few circuits left in case I add something else to the car like nitrous or another fan etc.