This same thing happened to me. I highly underestimated the extreme bioload of a Ray. My tank had been cycled but only using small fish as well. When the ray came it threw my tank into a mini cycle. I used Seachem Stability and followed the directions on the bottle. I added already established media from an existing tank to my sump and continued with routine water changes. Nitrite seems to take the longest in the cycle (or this 'mini-cycle'). I would test daily and watch the Nitrites slowly drop. Adding prime and also it was suggested to me to add Salt. I used 5 to 10 ablespoons of aquarium salt. However, I did not have any ammonia. If I read you correctly you did have some. This would make me nervous. I would continue with maybe smaller water changes 10%, but I can see what people are saying about establishing the bacteria. Also, I continued to feed as usual because it seems like an active and healthy ray would be eating. I just stayed on top of the water changes constantly monitoring the levels.
Good luck. Keep us posted.