Friend,
Great project for You and Your Dad!
My wife and I have owned our '91 6 cyl since new. Several of our troubleshooting and repairs have been wiring related. I.e. turn signals quit working, rear defogger quit, antenna, brake lights always on, engine sensors, etc. I purchase the factory wiring manual for our 4R for $20 from the Toyota dealer and it was a great investment.
Being and Electronics Technician, familiar with your vehicle, and having worked on our wiring, I think you would be far-better-off to troubleshoot your existing wiring system rather than replace it. Wires are just copper conductors and unless your vehicle has fire damage/melted wires, or salt water corrosion, I think you would be time and money ahead to troubleshoot what you've got. With the manaual and your dashboard opened up, you have good access to most everything and detailed information regarding.
It will take you some time and practice to get familiar with the factory wiring manual, but for $20 and another $40 for a good Digital Volt-Ohm meter, you would be making repairs rather than starting from scratch. As someone else mentioned.... in addition to the wiring you also have the connectors. It is no small deal to rewire connectors and the changes of inducing problems would be high.
As is with any Forum this is just my $.02 worth of opinion.
Again, Great Project for You and Your Dad! My Dad did similar with my brother and I when we were teenagers. For me it was 1972 Toyota Hi-Lux pickup, a project I will never forget!
Best Wishes for 2012,
Randy Graves
CdA, Idaho