Check your air (engine) filter box. They can crawl down the intake. I fashioned a metal mesh screen towards the top of the intake to prevent them from going down.
Same exact noise on my ‘24 eco boost fwd. the clicking comes and goes with no apparent reason. It will last about a week…loud audible clicks that I can feel through the brake pedal. More so when coming to a gradual stop than hard braking. Any luck at a different dealer? I’m in San Diego as well...