@Matthew Abate I too am going through my entire harness, but not to the same extent as you. I'm not replacing all the wire. Not that it's a bad idea, just not in my budget. I will be making repairs and modifications to support fuel Injection since I am going back with a RB instead of the L series. I am working with a fairly low mileage Z. I do plan to clean all terminals with Deoxit when it goes back together to ensure good connections.
You mentioned adding an additional fuse in one of the previous post. I thought I might share my current project. I have a fuse box I pulled from a S14. I plan to install in the same location as the original fuse box. I want the dash harness to remain as close to stock, so I'll wire it up with the original connectors. Ideally it's basically plug in play with addition of relays and extra fuse circuits.
There may be better aftermarket fuse box option, such as the Bussmann. This didn't cost me anything and has lead to me having a much better understanding of fuse box and wiring in the car. Your work here has also helped pave the way.
Hopefully everything works out. This S14 fuse box should be an upgrade from the outdated stock fuse box and offer plenty of expansion for in fuel Injection setup.