I know that American VS Jap Jags use at least one differant pot(i forget what one), and they are not interchangable, maybe you have jap control plate and are trying to fit american pot or vice versa?
I use CTS pots in all my guitars, and i have had to enlarge the standard holes slightly at times to do this, but as i never intend to use any other pots, and i mod my guitars to use not for resale value it dosent bother me in the slightest.