Hi Larry,
Not an expert on QC and the like, but checking the root radius of a thread is of no real value. The load bearing portion of the thread will define the degree of actual fit when engaged with the other part (nut/bolt) of the thread.
Do some research on thread measuring wires (three wire), go/no-go gauges and also comparators. There is a great deal of theory involved in these measurements and not something that can be answered with a simple "do this." It is very dependent on how much accuracy and consistency that you require. You may also want to chase down some NIST information on the topic.
Depending on your requirements, the go/no-go gauges may suffice. Certainly the most simple.