Could be heading for a disaster

So I think I am headed for a disaster, any thoughts or advice on the below situation would be appreciated.
 - We are at week 7
 - Fish are in tank
 - Plants are in the bed (cuttings and seeds)
Over the weekend I noticed brown spots on one of the fish.  It appears to be ammonia burns that are healing.
I have had the following chem readings

Ammonia 4 / pH 8 / Nitrite 2 / Nitrate 0 Temp 73

I checked again this morning and had this

Ammonia 4 / pH 8 / Nitrite 4 / Nitrate 2 Temp 74

The ammonia has been consistent at 4 and does not drop, ph the same.  Got this double Nitrite count but now getting Nitrates.  Vet says the brown is good in the fact the fish is healing but can not explain why no other fish is showing signs of Ammonia/Nitrite burns (apparently the condition is the same).  Coming from an aquaculture back ground we would just change 50% of the water and chem test the filter.

Well I have technically changed all the water over the past 3 days and everything stayed the same.  Now that I possibly could have slowed anything going on in the bed, I am at a loss as to what to do.

 - Should I remove the fish and let it run while the fish have r&r session in another tank, till everything drops, or let it cycle out as is?

Tank is 20 Gallon with 3 mid size comets and one small comet.
10 Gallon Growbed
475 Gph pump
Have not fed fish in over a week.  Need more info?  Plant cuttings are rooting and seeds are sprouting.  HELP.