The 'Fitting the hardware" instruction video 10.2 for the TL-1 for the PBG site, http://www.pitbullguitars.com/videos/#mg, shows them being screwed into the pickup cavity. But looking at that video it does look like they are machine screws, not pointed wood screws, and there are springs with the kit, so it should be easy to fit the neck pickup to the pickguard.

Remove the strings, scratchplate and pickup (you'll be able to leave the pickup wired in). Fit the two screws through the scratchplate, turn the scratchplate so that it's just leaning back slightly from the vertical, then on the underside of the pickguard, put a spring over each screw. Then (slightly awkward with just two hands so it can be easier to just fit one screw/spring at a time), screw the pickup on. Once you've got the pickup held by a few threads on one screw, then move to fit the other screw.

Fit the scratchplate back on the guitar and screw it down. Restring the guitar. Now you can adjust the height of your pickup by the screws with the strings in place, clockwise for higher, anti-clockwise for lower. I wouldn't raise it any higher than the lowest of the neck's wooden edges (not the fret height), but you can now play about with it until you feel it best matched the bridge pickup.

With the holes drilled in the scratchplate and the machine screws and springs supplied, it very much looks to me like video 10.2 is incorrect for the kit and it was designed to have the neck pickup mounted on the pickguard from the start. All the body mounted pickups I've ever had, have come with proper narrow wood screws with pointed ends, or for Tele neck pup replacements, a choice of wood or machine screws for body or pickguard fitting.