Ok, so you had the 400 and the 300 plumbed together, added the rock to the 300, fish got sick, moved them from the 400 to the 300 and closed the tanks off from eachother. Then you removed the 30 lbs rock and added some seeded foam?
Ok...
Still, in treatment tanks, I don't like to rely on biological bacteria to take care of the ammonia. I have Ammonia Alert badges in every system. They've saved my hide more than once. FWIW, AmQuel is much more concentrated than Prime, doesn't stink, and is cheaper.
Use the bottle to figure out a dose, but re-dose if the ammonia isn't gone. I know the bottle says something about not overdosing. If there is ammonia for it to "eat" then you are not overdosing. Overdosing is the addition of the detoxifier when there is no ammonia to "eat".