What's the advantage of the nylon rope vs just building the harness in the car? Substitute wire for nylon rope and you've skipped a few steps. Definitely make sure you're using the correct length of wire, if you always add 2" you'll have a nice clean harness. If you add "oh, about THIS much" you'll end up with a scraggly beast.
I've modified production harnesses and built from scratch. If this chassis already has the body wiring in place, I'd leave it and just add the minimal engine wiring. Factory engineers spent a lot of time and money designing what's in there. Of course, this is from the guy who lost the lead in the Targa due to a factory relay failing...
If you're doing the latter, the key is the fusebox. Get one with integrated relays, it'll be much easier and cleaner. Something like this:
http://www.delcity.net/store/Sealed-Mini-Fuse-Panels/p_803796
Start off by drawing your layout if you don't have a high level of comfort with your car. In your list, you left out the gauges, any interior lights you may want for servicing the car at night, radios, power for data loggers, aux lights, etc. Even a simple harness gets busy in a hurry. Assign relays and fuses to each circuit so you know how many you'll need.
Make sure you use color-coded wires. It's best if you stick to an existing scheme, such as the universal LBC colors or the chassis of your car. My Miata, for example, doesn't have much Miata left in the wiring harness, but I can look up the remaining circuits by color. You can use all one color of wire if you label the ends, but I find that's less useful if you're trying to chase a particular wire through a bundle when troubleshooting.
A good source for quality wire with the appropriate colors is a factory harness. I've torn down a couple and I just coil the wires up and toss them in a box. Then, when I need a blue wire with a white stripe, I go to the box. In my experience, even 40-year-old British wires are solid where it's been protected from the elements and heat. The Japanese stuff I usually work with is like new even when 20 years old.
Loom the wires using something you can easily pull on and off. I've started using velcro strips instead of zip ties because you're less likely to nick a wire when removing them - and you make less of a mess. You can buy rolls of velcro at HF and home improvement stores. Make sure the wires won't vibrate much, that will cause problems in the future. Where they have to move - such as the jump from chassis to engine - make sure there's enough slack that they won't get pulled loose with engine movement. Allow for failed motor mounts. And of course, make sure they can't rub and short out.
Use good quality crimp connectors with heat shielding. These are my faves: http://www.delcity.net/store/Heat-Shrink-Butt-Connectors/p_801794. Use a proper ratcheting crimping tool and you'll never have a problem. For example, this one or one like it: http://www.delcity.net/store/Double-Insulated-Terminal-Crimp-Tool/p_665741
Soldering is more brittle and not my choice for a high-vibration environment, although this is something people feel strongly about. I do know that I never see solder joints in factory harnesses.