Sounds like you've settled now, but for future reference, I've wired up that exact same pickup combination many times, and depending on the guitar and player—playing style, tuning used, string gauge used, woods, etc—I install them with either a 300k and a 500k pot, or double 500k pots. I can't think of a time that I have or would ever use either 250k or 1meg pots with that pickup combination.
The A2P is a much lighter and clearer pickup than many people assume, so my pick for that is always the traditional combination of a 300k volume pot and a 500k tone pot.
The Custom Custom has been wrongly represented by Seymour Duncan for many years, but people are now starting to get a better idea of how it actually sounds: take the Pearly Gates, up the output to 150%, and you've got the Custom Custom. For people using lighter strings and more classic amps, a 300k volume pot works fine, but for users of medium or heavy strings and/or oversaturated amps, I wire the Custom Custom with 500k pots for both controls.
In cases where the pickups will share controls, I typically allow the Custom Custom to decide whether the volume is a 300k or 500k pot; it's usually preferable to accept a little added brightness on a neck pickup than to have a slightly muddier bridge pickup, so if the Custom Custom demands double 500k pots, that's what the A2P will just have to put up with.
As line6man says, 1meg pots aren't a great idea because the taper is so inconsistent, even with a linear pot. Even if people want the increased treble and output from higher-resistence pots, I always recommend using a 'no load' pot instead, which is a 250k or 500k pot that simply clicks 'off' at 10, or a bypass switch, rather than using a 1meg pot.
250k pots can be okay with the bridge version of the A2P, when used with an HSS pickup arrangement. It's just clear enough for it. I wouldn't put a 250k pot on the neck version, though, and I'd absolutely never use a 250k pot with the Custom Custom; you may as well roll the treble on your amp all the way to 0.
