I got a mexican strat last week (hock shop) and the previous owner had put these custom pups in. The highs (6th & 5th) are so short they hardly pick up a tone. They're below flush of the pickup cover. The mids are like 4 mm higher and the lows are about 2 mm higher than the highs.

is there anything i can do to change the set up? (other than just flipping the pups around)
Well, depends. I assume you are talking about single coil PU's. Most single coils do not have adjustable pole pieces. I have seen a limited few that were adjustable from the bottom of the PU. Other than that it is possible they are installed backwards..
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