I've thought about this a bit for a few "projects" I've got in mind.  I read a few things on the web, sorry didn't bookmark them, but seems people get a big sheet of cardboard from a box and use this to try and keep the shape of the harness and to keep it flat in the plane of the playfield.  As I've studied mine - and they are all WMS machines, but I guess the others are similar - it seems the harnesses are split into three separate entities; one for solenoids, one for switches and one for lamps. Also they have been put down on the playfield in order, so it would be best to preserve this order. I think it was solenoid harness closest to the playfiled, followed by switch harness and then lamps furthest from the underside of the playfield.  The three harnesses are cable tied together at a few strategic points - I'd cut these to seperate into the three individual harnesses but mark with bits of string where they were joined to aid reassembly.

As you say, it would pay to label everything, both on the device as it is pulled off and on the playfield from where it is removed and take heaps photos from different angles. I guess you'd need to pay attention to the variety of hadware and where it is used to attach things, I did this by just sketching each area as it was dissembled.

With carefull attention to detail I reckon it is well achievable and will give you the ability to clean everything really well. Will watch with interest.