So my new modded guitar will have a stacked humbucker in the neck (seymour duncan recommends 250k pot), a single coil in the middle, and a real humbucker in the bridge (500k recomended).

So should I use 500k for volume and bridge pickup tone, and 250k for neck pickup tone?

it depends a bit on the exact pickups you are using but generally speaking the answer would be yes. Use 500K for volume and tone on the bridge and 250K for the neck and middle.
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