Agitating the sand the way you did may account for the sudden spike in nitrates and ammonia, Im not sure you cured the rock enough either. This may be your problem. The sands dead spot is not helping. I would highly reccomend removing any remaining live stock into QT, and start doing heavy water changes on the tank. Increase flow, add a powerhead to blow across the back bottom part of your stack to help circulate any dead spots that may be occuring. Get those nassurus snails too. add an extra canister fileter or HOB to help with filtration, that would not hurt at all either.
In short I think your best bet is to beef up flow, big water changes and beef up filtration for the duration until the levels return to normal, but if you dont get your livestock out, its likely going to continue to slowly die off, which is not helping the situation either. If you need I have a couple rubbermaid tubs, DIY frags racks and a HOB filter I could let you borrow. I used the tubs and HOB as a temporary flat while moving, have also used them as a temp QT. I also have a 250 watt metal halide you could boroow to hang above the flat so you have good light. If you need it let me know, Im leaving for camping early tomorrow morning so youd have to come by tonight to grab this stuff.