was the engine temp below 100 degrees when you adjusted the valves? when you did the adjustment make sure the engine was on TDC for #1, then turn and do #3, turn again to do #4 and final turn for #2 in that order.
I had a Honda Element that had a similar misfire on #3 only, after running the diagnostic checks it pointed towards a valve adjustment, after the adjustment misfire was gone.
Now you said the timing was off 2 teeth? how did that happen? if so there's a chance you may have a bent valve in that cylinder, but I would retrace your steps with the valve adjustment