If you are planning on putting a sound system in, now's the time. Speaker wires, rca cables, larger gauge power and ground for amp(s) etc. I would also leave a couple more 12v accessory wires than you think you'll need. At least 1 or two in the dash portion, then maybe one or two in the tunnel. You never know when you might want to add cable for a go-pro on the main hoop.
My current wiring harness is a rats nest as I've added and changed stuff over the last 4ish years.
As to the actual harness process. Plan for 25-40hrs of work depending on your comfort level with electrical work. It's not hard but it is methodical and detailed. Use Lonny's method of the big table. It helps having a lot of work area so you can stretch the harness out. Use a cleaner and some shop towels after you de-tape the original harness to make it less sticky and easier to see the wire color. I use a label machine to make the labels then put clear heat shrink tubing over them so they are protected and don't fall off. Solder and heat shrink every connection you make. Use weatherpak style connecters for your lights so they are solid and protected. Lastly, if you don't have the appropriate tools for adding connectors and stuff, just buy them. $150-200 worth of tools off of Amazon will make the job so much easier and is well worth the expense.
Just keep in mind, you are hacking like 60-70% of the factory harness out and modifying the remaining bits. You're gonna have a few issues and it will take some time but that's part of the fun of building a kit.