To add my thoughts suggestions to the already great advice in this thread:
If I were to do this again I think I would do a couple things differently. After replacing all the large boards I would not go replace all the individual boards in order as the instructions have you do it. Instead I would first install the BAG and interface boards in the middle then use the 2.0 wiring diagram in the manual and work from one large board to the next, plugging in the "satellite" cables and replace the individual boards with those cables in place so I could see exactly where to mount the boards, how to route the cable, etc. I'd work from each board in the order the cable progresses, I think that would be simpler and a little cleaner personally.
I'll also add that my kit did not have enough #4-1/2 inch screws and that screws from Home Depot are complete crap, they strip out incredibly easy! There was a bag of smaller #4s but those were never listed as being used in the instructions. The mounting hardware for my power supply was not #8 as the manual lists but rather M4 as Vireland stated, the #8s won't tighten down properly. Lastly I think they should include a new rubber mount for the Rainbow plastic that keeps that light pipe in place, mine very nearly ripped in two while I was taking it apart even though I was trying to be very careful with it.