I too suffered from a severe case of the shanks that nearly caused me to quit the game!!!
To answer some of your points
1) the backswing is started with the rotation of your core, so that includes your shoulders, stomach and hips
2) bad alignment can cause top's, if the ball is to far behind the bottom of the swing arc you wont be catching the ball at its equator first, you will be as you do topping it, it could also be to far away from you in the stance, try moving the ball forwards and backwards in your stance until you find the best place for good contact (For me the ball forward in my stance works best for consistency)
3) when lining up i use this drill, stand up completely straight, then flex your knee's to your normal degree, then hold the club out infront of you almost 90degree to your waist, elbows slightly flexed, then bending forwards from the hips keeping your back straight as possible, until you sole the club on the floor, this is where the ball should be for that club, as it changes for each club slightly, this should also ensure the club is soled to the floor properly
and as above check you weight distribution, i had mine hovering over my toes causing me to lead with the hosel and shank the ball, to combat that i moved my weight to my heels for a while and hit balls, then gradually moved it forward to the balls of my foot