If you changed our the filter without transferring any media, that could indeed be the cause. If that is the case, you threw out all the beneficial bacteria that was in the old filter. So you are having to start a new nitrogen cycle. That is very hard on the fish.
You are between a rock and a hard place here. The ammonia will be less toxic at a low pH, but the bacteria you need to process that ammonia and the resulting nitrite will have a hard time getting established in that acidic water.
You need yo raise the pH, but you will have to bind that ammonia first, as soon as possible, to prevent more harm to your fish.
Get some Prime and dose your pond. Then gradually and slowly raise the pH with baking soda.
As Mmathis said, clear water has nothing to do with healthy water. You can't see ammonia or other toxins in the pond. And your water is highly toxic.