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Pickup off Center

Hey, on my MIM Jazz, the neck pickup screw holes are drilled pretty low. With the factory pups in, the pup was centered, but when I put some Model J's in, the pup would not fit in the pickguard, and I had to grind a significant amount of plastic off the pup cover to get it in. Now there is a 3/16" gap between the top of the pup and the pickguard, and the strings are not centered between the poles. Has anyone seen this before? Is there a safe way to fill the factory holes and redrill them a little higher, or is there a reason they are there? Thanks!

I will post up a picture when my phone decides to send it.