Updating the situation.... After getting the ammonia pretty under control my water cow has died. He had a lot of spots like the ones in the pictures, it was pretty severe.
I post that to say this, I'm not sure that im still leaning towards ammonia. I had a large tree limb in the tank as seen below. After inspecting the tank with my wife, we found the same looking stuff that was on the fish on the backside of the tree limb. Last night we removed the limb and I will be doing a massive water change today.