JRS,
Unusual comment and observation.
Recommendation. Engine off, push clutch pedal several times, listen at various points pedal assy, at firewall, under truck at trans for any possible noise source, investigate a little bit, but sounds like warranty at dealership. Get it fixed or documented.
I don't know of a reason that you would have any hiccups in the pedal stroke on a 5,000 mile truck.
Do you feel it in the pedal or hear it or both?
Good luck.