I recently ordered an 11-screw Strat pickguard to go on my Squier Affinity Strat (MII). All the holes were close or right on. One was off a half a diameter and another was off that much and off at an angle from the factory anyway. The Squier screws were a bit large for a pickguard. Rather than re-do the countersunk holes in the nicely done Warmoth pickguard, I ordered a bag of ±20 Fender screws and just re-did the holes.
I started with a box of toothpicks and some wood glue, Titebond II I think. I took three toothpicks at a time and dipped the tips in glue and pushed them into the holes all together. I tapped them in gently but firmly with a small flat-faced hammer. Then I cut them off with a small flush-cut wire cutter. Once cut, I gently tapped them smooth with a flat punch, taking care to not mark the surface of the finish. That completely filled the holes and gave me a smooth surface to start from.
Next I put the pickguard on and used a thin awl to start a nicely centered hole and drove the screws in with a screwdriver. With those skinny little screws, I didn't need to drill a pilot hole. In fact, I did this while the toothpicks were still wet with the glue.
The pickguard went on much better than expected and even if the holes had been completely off, the same process would have been fine.