You need to draw yourself a picture. How can adding a shim between the mount and the trans lower anything? The trans is above the mount. The drag link is behind the motor plate a good foot or so. Raising the trans will raise the every part of the engine behind the plate. The further back from the plate the more clearance will be gained.Correct so if you shim the transmission mount,it's bringing the engine and transmission down making it worse.
Edit... if you are raising the transmission, it's lowering the engine .
If you are lowering the transmission, this will in deed raise the engine and give you more room in the centerlink.
Doug