Adam, I used White Knight white spray paint then a gloss lacquer spray over the top, about a billion layers of each. =D
I have definitely been taking away the paint from the neck pocket and pickups holes etc, and I know the reasonings for that.
I did do a practice go on a peice of scrap wood to get the feel but I unfortunately don't have the money to buy a kit just to have in ruin!
I don't understand what you mean by setting the neck up, what more do I have to do installing-wise to get it perfect other than sitting it in and screwing it in?