I have had some pedal bearings go, but I could feel something was wrong with the pedal thru the shoe sole.

I had a really frustrating intermittent noise a few months ago, I was unsure if it was the crank or a pedal, but it had a frequency that was identical to my cadence so I thought it had to be one of those. It did not sound like a seatpost or saddle noise. I eventually figured out that it was a small multi-tool in my jacket pocket that would bang on a little plastic box in the same pocket on each pedal stroke.

Do you have a kickstand or a fender that could be tapping on something? (Surly recommends against kickstands on LHT chainstays behind bottom bracket, but I have one on my LHT.)