I checked your Gallery, and was a bit surprised to see no live rock. This is more than likely why your having ammonia, ecspecially with the bio load from the puffer. 0.25 is not an acceptable range for ammonia,
it should be a constant 0, the same goes for nitrites. All I can say is do a good 50% water change, and try to get a hold of some good cured LR
. Id also put in a DSB
if possible. I have two perculas and my smaller one stopped eating for a week, then started to eat again. Since you have ammonia readings id say that is the cause of their health decline, and loss of appetite. Best of luck, and remember the more rock you have the more biological filtration, and that is the key to better water.