As long as each u-joint has some angle, 3 being the most, and that includes up and down and side to side, then you will be all right. From what I have read, if the transmission to driveshaft angle is about 2 degrees, then the driveshaft to pinion should also be about 2 degrees. This is where the angle finders come in handy. The angle of motor and pinion to the ground makes no difference, you want to know the angle between the driveshaft and each end. A u-joint needs some angle so the inner bearings get worked around, if its straight, the bearings just get looser as they dig in.
Joe