I'm not absolutely sure if it's the pedal. The bike is a singlespeed EighthInch Scrambler v2 with Origin 8 square taper cartridge BB, 107mm. Cranks are EighthInch "track" cranks, 165mm. And the pedals are cheapo WellGo track pedals, that's the reason I think it might be them.
But, about a week ago I was trying to figure it out, and I noticed both cranks looked farther out on the bottom bracket than normal, I got out the torque wrench and sure enough the both pushed in nearly a whole centimeter. But the clicking has since continued and gotten worse. My lady thinks it might be the freewheel but I doubt it, it's brand new. The entire bike was built up from scratch about 2 months ago, it probably has a couple hundred miles on it.