How high was high (the ammonia) and for how long? This is a very toxic chemical and conceivably it caused enough internal tissue damage to result in eventual death - in spite of the neutralizer added later. Ultimately, it may not be known what exactly happened - so the place to start I think is to re assess your whole set up & whether or not its adequate for size of pond and number of fish.
One thing that puzzles me is what all these gaps are, where the fish were hiding - you might want to seal those off somehow. If water and oxygen is not freely circulating thoughout the pond you could have dead zones which harbor bad bacteria - not good.