Did you attend a workshop recently?
90 deg body rotation position belongs to the 'Old School' of TI and I don't believed current TI workshops/books/dvds teaches them anymore.
As for your shoulder pain, it could be due to you are initiating your rotation from your shoulder first then abs muscles. If you could visualize dragging forward a bowling ball with a thin gage wire in water and something will soon bound to break . Maybe you could think of the whole body rotation process with your shoulders (arms, hands, etc) as the tracker, your legs is a stablizer, and your abs/core muscles is the rotator or power house.
Hope this helps...