All your options have merit. Several have used the universal harness with success and there is one company that does make a 6v version with heavier ga wire
http://stores.ez2wire.com/-strse-37761/AMC-Jeep-Chevy-Chevrolet/Detail.bok . On the cut and replace with modern the one thing to remember is that even though they look good, the insulation is still 60 years old. As you mention, they may soon deteriorate if exposed. In addition, you have also doubled the chance of a future bad connection somewhere at a splice.
I have built harnesses out of modern wire and it is a PITA but probably the cheapest. Aside from taking some time, very do-able. I think the easiest way is to have a sheet of plywood, lay the harness out approximately the way it is in the car, then use bent over nails to hold things in position. That way you can remove and replace the wires one at a time.
Check out the Rhode Island Wiring site
http://www.riwire.com/ on the more about us page for some ideas on that method. They also sell correct wire and terminals by the foot as does YnZ Yesterdays Parts.
http://www.ynzyesterdaysparts.com/catalog/ if you really want to do it properly.
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