Re: ngd!! well body at least!
When you want to mark holes for drilling, stick paper masking tape on the guitar and do your marking on it gently with a sharp, soft lead pencil (harder lead can make marks in the finish). I'd suggest getting the neck and fitting the tuners first, and attaching it to the body without over-tightening the neck screws. Then you can put on the two outside 'E' strings and they will act as guides so you can line everything up (the neck may have some side-to-side play in the pocket ... sometimes it can be best to have the pickguard loaded with pickups and drop that in place too, to make sure the pickups are centred under the strings).
You will definitely need a drill press or something similar to get the bridge mounting screws to be perpendicular to the top, otherwise there is a likelihood of the bridge binding on the screws when using the trem arm. If you can't find a way to guide the holes at home, I'm sure any cabinet-maker's shop or engineering shop would drill the holes for you very cheaply, assuming you've marked the locations and can either tell them exactly what size holes you need or have one of the screws with you so that they can select the correct size drill bit.
For touching up the chips in the finish, try nail polish (check the compatibility by testing a spot in the trem spring cavity or any other area with paint that will be hidden when the job is complete). If the nail polish is compatible and the existing finish is thick, build up the repairs with a few coats and then level and polish them with fine grade abrasive papers and polish.
