Quoted from Dante:

Pictures, pictures, pictures. From every angle, before taking apart, during and right after you remove the part. Then take all of the pictures and back them up in two places (learned this the hard way with a hard drive crash).
A notebook. Sketch out connections or note the order things are assembled
Get a lot of ziploc baggies and a sharpie. Bag and label as you go to keep track of everything. Tumble and polish in batches will help ensure everything is accounted for.
Start a list of parts early and order extras when you do. Nothing is more frustrating then just getting your order from Marcos/Pinball Life and then realizing that you need one extra thing and now need to wait another week and eat another $10 in shipping.
Don't push it. Work at a good pace, but know when to quit. Nothing sucks more than f'n up a part/plastic/playfield than when you didn't quit when you were too tired/not into it at the moment.
Soldering/wiring. I snip all coils and add molex connectors when I reassemble. GI and other smaller connections, I leave intact.