I think your intake pipe is too long in relation to your exhausts height. In the convection loop, air flow tends to follow the path of least resistance, so when you ran with the bottom intake open, you saw better response in the air flow, or air draw, as opposed to the vertical intake. On my DrumPit I have the one vertical pipe, 1" dia., choked on most of my smoking sessions to about half of the opening of the pipe diameter and I maintain temps around 225*-250* consistantly. My exhaust is a single 2" pipe that I position opposite the air intake. I don't think the elbows I have on it make any difference in the flow.
My intake pipe height is below that of my exhaust pipe height and that may
aide in the convection processes. I hope my rambling helps!!!!