Ok here is your issue.... Humbuckers want to see 500K pots, singles want to see 250K. If you use all 500K, the singles will be brash and harsh(not musical at all), but the humbucker will roar. If you use 250K pots for the singles the humbucker will be muffled and choked up.
What you need to do is wire up a resistor across the 5way (assuming you are using a megaswitch) so that the singles "see" a 250K load, while the bucker only sees the 500K pot value. ----EDIT- I just checked and since you're using a hot rails, which is a S size humbucker, evident;y the duncan site recommends a 250K pot. I've included a link to the wiring diagram.
This will be much easier for you than the other method I mentioned of wiring in a resistor. seymourduncan.com/images/products/electr... I've also enclosed a diagram of how to do it using a mix of 500K pots and 250K along with the 470K resistor, that tricks the singles into seeing 250K from a 500K pot.
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