Chris,
I haven't had any pedals making funny noises, but I tend to think that the noise behind your left ear is the doors. I had the same problem and so did a lot of people. I noticed it mostly when the cab was flexed. My noise wasn't really a click though. It was more of a rattle and squeak (the doors rubbing against each other). Took it to the dealer and they adjusted both driver's side doors and lubed them. No more noises! I hope that's what the problem is.
Oh, besides the doors being "loose", for lack of a better word, both of my seatbelts were replaced because the driver's side belt extender was squeaking in my left ear and neither retracted worth a darn.
Good luck,
Andy