If possible you should not let the ammonia get over 025ppm
That'll be a typo, there, at 25ppm, you'd probably be smelling something! She meant 0.25ppm.
Is stirring the gravel a good idea? There are food flakes in the gravel, if I stir the gravel the flakes and stuff come up and then do a water change by collecting the dirty water.
Stirring the gravel is a pain, because you want to keep the gravel basically in one place. Get a gravel vac, when you do the water change, vaccuum up the gunk off the gravel at the same time.