The urine/ammonia is the natural result of the mold. I've not made a cloth-bound cheddar yet, but as I understand it, most of the mold should have stayed in/on the wrapping, not getting much down onto the cheese itself. You may need to use more layers and/or more lard in your wrapping - ?
I agree with airing it out for a day or two, and/or scraping off the mold as needed. I think I'd wait to cut it until I had done the latter, though.
