How to verify the pitch #of nuts?

I'm confused, true position has nothing to do with thread pitch? 

But to confirm the pitch of a threaded feature you can do it many ways, with varying degrees of accuracy. 
I would recommend a thread plug gage.
A pitch gage set (cheap and easy)
Make a mold of the part and check it with an optical system and measure it... 

Plug or ring gauges would be my recommendation as well. The only way I could picture manipulating a TP of a threaded feature would involve a MMC condition and changing the nominal without reporting the result to force bonus tolerance that doesn't exist. I don't think that's even possible with Getol now though.

I am curious about MMC condition with NUTs, Does any drawing applied with this?  The thread nut is totally different from hole, how can MMC condition work ?

The MMC bonus needs to be calculated from the effective diameter of the thread, which it is almost always impossible to measure on a CMM.  The only exception to this would be if there is a note on the drawing saying to use the minor diameter, but then, you would need to ensure your probe contacted on the crests of the tread.

The MMC bonus needs to be calculated from the effective diameter of the thread, which it is almost always impossible to measure on a CMM.  The only exception to this would be if there is a note on the drawing saying to use the minor diameter, but then, you would need to ensure your probe contacted on the crests of the tread.

Thank you. I agreed with a PE on no MMC condition with Nuts last year.