I'm not trying to piss in your Cheerios, but you would be very wise to replace as much of the harness as possible with a replacement made by someone else. I'm great at electrical. I got a perfect score on my last ASE electrical recertification exam. I think electrical problems are fun. And even I won't try and patch individual wires when the harness has damage like you've described. Let me tell you why.
Every inch of every wire that has any signs of damage, must be replaced. If it got hot enough to burn off the insulation at one point in its length, then the entire wire is suspect of having melted into another wire, but that you won't be able to see (in a harness). Moreover, the wire becomes forever damaged when it gets that hot, and is much weaker now than it should be. When you splice in new pieces of wire where you see problems, you are still keeping damaged portions of that wire in other places in the car. Doing such is just begging for more problems to occur, possibly setting the car on fire (that's what happened to my '69 Chevelle SS396 back in 1984.
).
Replacement harnesses are not cheap, but neither is buying a new car because yours caught on fire because of a short to ground in the brake light circuit where it tucks underneath the carpet.
I would never try and discourage someone from working on their own car, but rather than splice and patch this system, save up your pennies and find replacement harnesses for all of the affected circuits.
Of course, that's just my opinion.