Follow Grigg's advice, it will work just fine. U-joints need some angle to work right, ever look at a long straight truck or box truck? The driveline goes up and down at each joint.
If the transmission tail shaft is pointed down 3 degrees, the pinion should be pointing up 3 degrees, or close to it. Side to side as you have isn't much of a problem, its most likely only a degree or so off. Joe
