Time. Substrate can bring in dust, etc. Also, since you're showing ammonia and there is an off chance that the thing is building bacteria again it could well be a bacterial bloom.
Nothing. They are normal when the biofilter is trying to (re)establish itself. That may or may not be the problem, but it's what I would lean towards right now given that you're seeing ammonia and covered your old substrate, which could cause some anaerobic pockets in the old gravel, etc.