Willem, there's alot of questions there. Most builders paint the neck and body separately mainly due to being too bulky to work with and hang if you glue the neck in early in the build. You should be able to get a smooth transition. I'd try and sand the marks out of the fingerboard, you can wrap say 240 grit paper around an eraser will curve the same shape as the radius of the fingerboard.
As for the black paint for the headstock, you may end up using half the can if you spray several coats so I wouldn't worry about the shelf life of the can, will more than likely have to throw it away after a certain period.
As the others said prime the body and neck before the white coats. Generally spend a bit more on the spray cans will be a better quality. Post any photos of any problem areas of the build will give us a better idea to get the best way to fix any issues