The answer to all those questions except the last one is, "it depends." You really need to lay everything out on paper and see how deep all the routes need to be. Pickups are different depths, necks are different heights, etc., etc.
Where to get a neck pocket template? Make your own, or you could look on eBay or stewmac.com.
The answer to the last question is "Under no circumstances should you spray lacquer (or anything else, really) without a proper respirator." Nitrocellulose lacquer will do serious harm to your lungs.