Not done one for my bike (yet), but i have built looms from scratch for two rally cars and a road car in the past.
I would echo what bryan & Raul have said, slowly and methodically is the way to go, use the old loom as a pattern to get your lengths roughly correct. As Raul says, avoid the connector blocks, run your wires A-B where possible. The blocks were just put in by the factory to make assembly easier and allow different options packs to be used (see the thread about the spare green wire).
Also, on any connectors you do retain, say for the lights, ignition pack, switchgear, etc, give them all a good coat of dielectric grease when assembling.
Oh yeah, and document everything as you do it, not afterwards. As well as diagrams make a schedule of your chose coding AND STICK TO IT! It makes life so much easier in the long run
PS: Bryan, you have any objction to me pinching your heat shrink colour coding method? It must be far less time consuming and more durable than my previous paint or tape methods!
PPS: For anyone who's interested, it is possible to remove nearly 80kg (160lb) of ancillary wire & connectors from a mid 90's UK spec hatchback and still have it run & operate correctly
I dread to think how much unnecessary rubbish a new car contains