Hi,
I use the Chopper T in a Tele with 250K Pots. Usually I roll off the tone a bit, because there is still plenty of treble with 250K pots. If you like it really bright, go for the 500K. If not, the 250K should be fine. Concerning polarity, I cannot tell you exactly, because I don't have any experience with Harmonic Design pickups. However, with a Tele it's so easy to remove the control plate and swap connections, that I would simply try it the way you expect it to be. If it turns out to be wrong, it's a matter of minutes to change it.
Hope that helps,
Jörg