guessing my fanatical wc regime is what kept the bacterial count low enough for the rays to fight it off? But now that the aro is harrasing the one ray he is showing symptoms due to a lowered immune system.?
I think that you just hit the nail on the head.
I concur with Bret, use the 3% epsom salt solution on the aros food (to kill any potential hexamita/spironucleus) and begin treating for a potential bacterial infection for ALL fish. The aro at this stage does appear to have a prolapsed rectum, and the epsom salt in the water, and in his food will help resolve that. Kanamycin is sold by Seachem under the name Kanaplex. You can mix it into the food as well.
http://www.seachem.com/Products/product_pages/KanaPlex.html
Try Henry & Nature's Corner, or Big Al's for Kanaplex.
Another alternative is Maracyn and Maracyn2, which will treat both gram positive AND gram negative bacteria, but I believe they also affect the bio bacteria, and the last thing you need right now is a major die off of the "good" bacteria in your filters.
Also, most bacterial problems in fish are gram negative, so for now I would advise keeping things as simple as possible. (use Kanaplex)
The red streaks in your ray appear to be bacterial hemmorrhagic septicemia. (a gram negative bacteria) Your vet isn't going to be able to tell you anything with any real certainty unless he/she takes a culture, puts it under a microscope, & knows what they are looking for.
More info on gram negative bacterieal infections in fish, including bacterial hemmorrhagic septicemia.
http://www.cichlid-forum.com/articles/diseases_bacterial.php
HTH
Neil