Turn vice over, accurately (*) mill a slot in the base for a key to engage your Tee slots, revert to vice correct way up, and slide / press the key against the wall of the Tee slot as you tighten your hold down bolts. If your slot is accurate then the vice should already be set parallel.
(*if you grip a piece of flat bar in the vice jaws before inversion, and slide it against the Tee slot wall your alignment should be bang on)