When I did mine i first mapped out the order in which things were to be done...but then again I'm kind of particular about my projects. I knew about how long it would take when I had to farm out work so that I could work around the schedule to maximize my time. I make a gant chart and keep track of status on a couple whiteboards in my shop...i'm anal i know.
-- strip bike to a roller
-- make modifications (frame kit for me, try your gsxr front end, etc)
-- finish striping everything down
-- sandblast, pc, paint, whatever
-- rebuild engine
-- wiring
-- finishing touches
Copious numbers of ziplocs and clear boxes. Do things in groups (frame work, engine, suspension, etc) that way you dont have too many irons in the fire at any one time.
Other than that; take your time, label everything, take pictures, research anything you dont understand, drink lots of beer, and have fun.
One other note...powdercoating is all well and good. However, after having mine powdercoated I kind of wish I hadn't as I dont have any way to touch up future mod's or accidents. The 350 I'm building is painted and it's much easier to deal with. Looks pretty close to the same as well. Not to sway you one way or the other. just food for thought.