Just for clarification - it seems that you may be using a Gecko G540 driver with a 10 microstep setting, and you are looking at calculating steps per inch? If so, my math comes out the same as yours.
If you work backwards from 9948, you come up with a pitch of 4.974 mm.
So I'm wondering just how close to 5 mm the pitch actually is. Could you measure that (or have you measured that) by counting off a larger number of full revolutions and using the calipers to get the linear movement of the nut, then dividing by the number of revolutions to get a more precise approximation of the actual pitch?