I think this is part of your problem. That is too long of an acclimation. From the time the fish is bagged, ammonia is rising and ph is dropping. You want to acclimate for no more than 20 minutes. I QT all my fish and set my salinity and temperature to that of the tank I bought the fish from. This way, the acclamation process is dramatically reduced. Over the several weeks in the QT, I raise the salinity to match that of the display tank, making that transfer quick as well. I do a water change on the DT and use that water to do a water change on the QT. Over time, the QT water parameters will match that of the DT.
Any ammonia is toxic. It should read zero, if not, it will stress the fish and at levels of .25, it is lethal to most salt water fish.
For the nitrogen cycle to be complete, the tank should be able to process 2ppm ammonia is 24 hours or less. If you dose pure ammonia from ace hardware to a concentration of 2ppm and it is zero in a day and nitrites as also zero, then the cycle is complete and your bio filter is solid and the tank at that point is ready for the first fish.