AeroPod, PowerPod and Newton

As far as getting accurate wind measurements, would I be better off using a low-angle stem mount which gives the unit about a 12-13 degree UP angle or a high-angle stem mount which gives the unit about a 6-7 degree DOWN angle?

Low angle is probably best, mostly because it is easier to read. In either case the iBike 2 software and calibration procedure will make the necessary corrections to the wind scaling factor.