Tim, if its only the 5 way switch is making the black pickguard proud I'd carefully drill some holes around the area it is bottoming out, just drill small amounts at a time and test the fit.
With the pickguard/bridge fit, is the neck in place in that photo so the pickguard is close to its final position ? You may have to carefully file the edges that aren't parallel or trace the white pickguard shape and try and replicate that