Noise is a funny thing, I had a noise once that was driving me crazy, only under load, up hills. It turned out that when I was sliding back on my seat for power my thighs were rubbing on the velcro saddle bag strap around the carbon post. Boy did I feel dumb:blush2: after taking it back and forth to the bike shop thinking something was wrong with my bottom bracket.

On other occasion I was getting bad noise under load only. It turned out that my Sram casset was loose, once tight no more noice, and I could go up 1-gear higher on the big ring.

 

I had the similar issue with my Cervelo R3 SL (Sram Red, ZIP 303) and it was driving me crazy about 6 weeks. The creaking when standing turned out to be coming from the bottom bracket (which I cleaned, regreased and re-torqued to fix) and the constant clicking on each pedal stroke was resolved with one little drop of oil on the rear quick release hinge. I am now back in love with my Cervelo - it was dicey for a while.

 

I've experienced a click I was able to localize to the large gear of my (triple) chainring. I was able to correct it with some slight derailleur adjustments to the front and back. They were just slightly off and causing the chain to hit one of the rivets on the ring. Another contributing factor was my frame itself, and it's not something I can correct. My Vitus 979 frame has a fair bit of flex at the bonded joints. If you're riding a bicycle with some flex in it, that could be the cause. There's really not much you can do about that except to be extremely careful with your drivetrain adjustments, and keep an eye on the chain and the teeth of the chainring for signs of wear.

 

Did you check the pedal bearings? From what you wrote it seems like you just took off the pedals and re-torqued them onto the cranks.

I know the OP's issue has been resolved. But I just bough a brand new bike and immediately changed the stock pedals with brand new pedals. There was less than 10 miles on the NEW bike and NEW pedals when I developed a click mashing down on the left pedal. I disasembled the pedal and applied some good waterproof grease. No more click.

 

The fact that the click occurs at the same point in the pedal stroke for both feet makes me wonder if your shoe is where the click is happening. Or, for that matter, if your rear shoe may be flicking the front derailer cable. Good luck. You've got quite the mystery going.

 

Check your cable housings where they meet the stops on the front of the frame. They make some pretty horrible clicking noises when the inner wires poke out and rub against the ferrule.
Grab the housings and twist them around. You'll know it if you hear it.

 

I spent all season trying to kill the click. It ended up being a chainring bolt. Now I own that little chainring tool, so it will never happen again!