Stingergirl88 - In my experience three and a half weeks is not really long enough to effectively cycle a tank for rays. Especially if all you have been doing is adding stability to your tank during the cycling process (and there after)? It is my understanding that these products contain nitrifying bacteria (I have never felt the need to use them), what are these bacteria feeding off in a freshly set up tank with no ammonia source? What would be the difference between adding a cap full every few days for 3 weeks and just dumping the whole lot in at one go? Not a whole heap.
You are much better of doing it 'old school' - seed your filter with some media from another filter, and add an ammonia source and test water to watch ammo drop, becoming converted to nitrite -> nitrate. Then add more ammonia and repeat the process until you are happy that ammo is being effectively converted. There is absolutely no way that your tank should have no nitrate, if properly cycled with a ray in it. It is that simple. If there was ammonia present (and there will be with a feeding ray) where is it going, it doesn't evaporate, and nitrite and nitrate are 0?
At the end of the day your ray is feeding so that is a great sign, I just simply don't rate the way you have cycled your tank (my opinion/experience), and your water readings would affirm this as strange as they are. Granted you have experience with fish in the past, but rays are a 'different kettle of fish', they produce far more waste than the average keeper would appreciate and can be very sensitive to poor water quality (especially at a young age and in a new environment). Take it as a learning curve, don't keep rays in very new tanks (3 weeks worth of cycling with an off the shelf bottle is not sufficient).
I can't help too much with the treatment of fungus - we have different medications in Aus and I have never had a ray infected with fungus. For the store to say that it is a common issue is not really great either, if properly cared for I wouldn't say it is common for rays to be affected by fungus.
Good luck with your ray.