I was told to add GEN-md, ATM colony. I was told to add food to the tank for the first week without any fish in, after that week, ammonia, nitrites and nitrates were at zero.
when you first did this did you ever see a spike of 4ppm before seeing things go to 0ppm
I'm thinking you never even had a spike that would have kick started the cycle .
Remember the test kit is needed to see the spike at the beginning 4ppm than again at the end of cycle to see when the nitrites and ammonia are are at 0ppm
I'm still thinking that this tank never cycled correctly everything you say leads to that
I do understand you went with what the pet shop told you you followed what you were told . the food alone didn't give you a spike big enough to start a proper cycle , this is why we always advise to use a deli shrimp this will always give you that spike your looking for to start a cycle, see link
Cycle your salt tank - Aquarium Advice
I would bite the bullet remove all the stock put in qt and run a new cycle the correct way
remember your stock is in Qt you will need to do daily water changes to keep ammonia levels down
once you do this you should resolve your issue you can reintroduce your stock and let you move on and enjoy your tank rather than stress out
I removed the remaining fish and placed them in a quarantine tank. The pet store advised against this.
what I get from this is they were trying to get you to do a fish in cycle , yes they can be done but very hard on the fish , The fish less cycle is more thorough with the introduction of the shrimp it will produce ammonia and nitrite spike 4ppm than after the beneficial bacteria forms the ammonia and nitrites will be consumed by the bb bringing you to 0ppm and your cycle is complete , your bb will become stronger as your tank matures. your fish will be happy and your tank will thrive,