my suggestion to you would be, leave the other pickups and keep the switch on only the invader. It's a really hot pickup so it will so fine on its own, the other pickups won't effect the sound, and who knows? you may want to use them later. As far as the woodworking is concerned, unless you have the money for a new guitar DO NOT DO IT YOURSELF! You may just want to spend the money on a Tom Delonge strat and avoid the hassle altogether. It has the exact setup you want without the other pickups and a solid, one hole pickguard.

P.S. I'm not exactly sure, but guitar center may have a pickguard with a single humbucker hole. You could go check with them.