I can't believe (actually I do, because that's what happened) that you replaced tree pedals without making a difference. SOP for a synchronous click is to replace pedals to eliminate the pedal and pedal thread. That should entail cleaning and greasing the thread, or at the very least, cleaning the face where the pedal flats meet.

I could see leaving a bit of dirt there once, but it's hard to believe that three changes didn't clean it off by accident if not intent.

BTW- Though i still don't use them, I understand that pedal washers seem to help with this issue.