If it was me, I'd lay out the body positions for the pickups and use a
template to route those first. When the pickguard material comes, cut it to shape, bevel the edges, drill the mounting holes, countersink 'em and mount it. Drill holes large enough in the middle of the pickup locations for an edge follower bit, and route the pickup holes at that point. That way you know they'll line up perfectly. If you cut the pickguard's pickup holes before the body's, you've got the tail wagging the dog and that's no good. Pickguards are easy to do over. Bodies, not so much.