To be honest, unless you are using a brick that is higher wattage than the default one pico-box supplies, you probably don't need to mod the wires. We're probably just being a bit OCD here and I want my wires to be sleeved to about the same thickness.
If you still plan to go through with it, I would suggest buying the right tools. Most of the stuff you can get from a reputable store like MOD ONE (
https://mod-one.com/). They will supply you with:
- New wire
- New pins
- New molex connectors
- heatshrink
- sleeving (optional)
- crimping tool
- pin removal tool (if you plan on reusing anything)
You'll also probably also need a soldering iron and some solder and I would recommend that you get a nice wire stripper to make things easier and more uniform.
The basic idea is to use uninterrupted runs of new wire wherever possible and only splice (connect two wires together) when you absolutely have to. When you want to splice, make sure you solder the two wires together (look up a youtube video for this one).
As far as using new wire.
1) Cut it to the length you want
2) use a wire stripper to strip off 1/4 inch or so of insulation
3) use your crimper to crimp on the molex pins
4) sleeve it if you want
5) throw on the heatshrink
6) activate heatshrink
7) insert molex pins into connectors
Since you'll basically be recreating the original harness more or less, you can follow their pinning. If you want to learn more or if you want to alter it more, you can always look at a pin-out diagram.
I've only been asking other people for help, so I figured I would try and contribute. There are video guides out there too if you want a video walkthrough. It's fairly simple, but you need patience to get good results.
Hope this helps!
I think he's on his last run (if I understood correctly) 
