making wiring harness from scratch

One thing that concerns me about the elevator cable is its heat resistance. Should be fine from the firewall back, but you might want to use high temperature wiring like TXL or GXL under the hood. There's quite a big difference in how the insulation holds up to high temperatures between different grades of wire.

Checking in on this thread.
A few questions as well:
What gauge wire is a typical a-body wiring harness?
Is it all the same gauge? (dash, under hood, etc)
What gauge is the starter, battery, alternator wires?

There's a lot of different gauge wires - your best bet is to get a factory wiring diagram, which will have them all listed.

I think the bulkhead connectors are the same as the other connectors throughout the car, is this correct?
Also, I have seen the connectors on e-Bay.

The bulkhead connector is its own animal - it's probably in the same series, but it's not the same connector itself. If correctness is not an issue, I'd be tempted to eliminate the factory bulkhead connector, and either use a more modern design or just run the wires through a firewall grommet like modern cars do. They're one more thing to break.

I am thinking it might be best to replace the colored wires with the same color, but I have had zero success finding the correct colors wire. Any one have any suggestions?

If you're not sure what color you should be using, again, you'll want the factory service manual diagrams.

If you're not able to find the right wires, you might want to try Waytek Wire - they have quite a selection, and in the right grades. We've got a lot of their spools hanging on the wall where I work. Biggest problem is it can get expensive to build a single harness, which is why some of those prepackaged kits can be quite helpful.