Hi there, just saw this however there is a couple pages now that I have no plan to read through so just to answer your questions in case no one else did...
When you bring over the old sand, there could be lots of gasses etc in there that normally would not be released into the tank. There are also all types of bacteria and depending on how deep the sand bed wad may even include some anaerobic bacteria. Disturbing that could cause massive die off. Also depending on how it was moved, could have caused even more die off. On top of that all the detritus that comes over to the new tank, would still need to break down. This wouldn't cause issue in the first few days, just like if the tank were brand new with all brand new items in it, and you tossed in nothing but a dead shrimp. There would be no issue until that shrimp started to break down, then you would get ammonia and your nitrate cycle a few days later. Sound familiar?