Ok so as we narrow it down, heres my thoughts:
1) The pink/red belly would indicate a bad substrate, but as you said it is bare.. This could only mean one other thing; Ammonia Burn. I see alot of freshly imported rays have this problem, especially when very young. It might be a trait of a very skinny and juvenile ray, but I would say the Ammonia in your tap water is the cause. I am unsure of how much it could also effect or damage the disc region.
2) The comment about the Filter 'pushing' him around the tank might indicate a stress factor. Although its not good to have any 'dead zones' in your tank, he might be seeking refuge just to relax and not have to fight the current. If he hasn't slept in days because of this, it could of caused some serious stress issues.
3) Rejection of food is a very bad sign, especially black worms. It could of came from the Ammonia, Internal parasites, or acute stress from tankmates and/or no refuge areas.
Hopefully you can take some of this and alleviate anything.. But at this point, there is not much you can do. I am a big fan of Salt when rays are stressed, and some might even say I over-do it, but I have never killed a ray from salt overdose. Keep in mind, they evolved from a SW fish and should be able to tolerate high salt levels, pH and hardness on the other hand is a different situation.