The Λ-doublet transitions in CH at 3.3 and 0.7 GHz are unusually sensitive to variations in the fine-structure constant and the electron-to-proton mass ratio. We describe methods used to measure the frequencies of these transitions with Hz-level accuracy. We produce a pulsed supersonic beam of cold CH by photodissociation of CHBr3, and we measure the microwave transition frequencies as the molecules propagate through a parallel-plate transmission line resonator. We use the molecules to map out the amplitude and phase of the standing wave field inside the transmission line. We investigate velocity-dependent frequency shifts, showing that they can be strongly suppressed through careful timing of the microwave pulses. We measure the Zeeman and Stark effects of the microwave transitions, and reduce systematic shifts due to magnetic and electric fields to below 1 Hz. We also investigate other sources of systematic uncertainty in the experiment.