I got the clowns from a LFS I don't go to anymore. When I first started my tank i didn't really know anything. I'd never go back to that store and buy fish. The guy who sold me the fish gave me the two clowns and one tang including a bottle of bacteria. He said dump it in the tank and it'll cycle instantly. Three days later the tang was dead and the clowns were dwelling on the bottom gasping. I brought the clowns back so they could recover while I was looking for the problem. The guy from the LFS said it wasn't ammonia it was something else. He wanted me to believe that I poisoned my fish by using some kind of chemical in the same room (air fresheners or whatever, even though we don't use that stuff). He looked at the dead tang with a magnifying glass and said 'Look the fins are damaged, that's a sign of poisoning!!!'. This guy sold me unhealthy fish and screwed me over with that bottled bacteria crap. In a new uncycled 40g tank, three fish, that was too much. The issue was ammonia. I somehow get the feeling that my problem is coming from the rocks I put in the tank. I bought it from the same store. I still have diatoms even though I use RO/DI water. I can't get my phosphates to go down. I bet they're leeching from the rocks. My nitrates have only dropped to 40ppm. I can't get them to drop more. I added some of that NoPox stuff and now I have super cloudy water. Probably a bacterial bloom. I don't know man this tank is a pain. I think once my nano is up I'm going to shut this sucker down.
Bummer! I'd say don't give up, sometimes you're just around the corner from getting on the right track. Though with rock leeching phosphates etc., that's going to be a tough one.
Also, bacteria bloom is most likely from No3Po4-x. Make sure your skimmer is going full blast and you have plenty of surface agitation. Bacteria blooms can deplete water of dissolved oxygen pretty quick, but having a skimmer etc. to put more oxygen in would save it.
You should probably stop dosing, maybe try running a cheap UV sterilizer (I just battled back a bacteria bloom too). Green Killing Machine works well!
Start dosing again after things clear up. I'd start with a very small dose, and increase over a few weeks until your levels are set.
If you run GFO, chaeto, and use No3Po4-x you'll eventually finish leeching your rock of all the junk. You could even use lanthanum chloride to quickly bind phosphates (be careful, read a lot about it before using).
Another option is yes, shut it down. Though you can do a restart the right way. It might be better in the long run. What I've seen work:
1. Take rock out and put it in a mild bleach bath (read more about it)
2. Give it a muratic acid bath (read about it)
3. Take a strong brush and rinse all the dead junk off the rocks
4. Let all the rock dry for at least a week (make sure it doesn't get rained on)
5. Put the rock in a tub of some sort with RO/DI water and a pump. Dose lanthanum chloride to bind to all phosphates that leeches out. This keeps it from being reabsorbed into the rock. Do this until you can stop dosing lanthanum and the phosphates levels don't rise anymore.
6. Rinse the rock out in RO/DI, let it dry for a few days, and then start up your display tank again
7. Cycle by dosing ammonium chloride to 2ppm, and use BIO SPIRA or Dr. Tim's One and Only to build up your bacteria. Once your ammonia and nitrites fall to 0, dose 2ppm ammonia again, and repeat until you can get your ammonia/nitrite down to 0ppm within 12 hours of dosing 2ppm.
That should do it.