I will be shocked if your cories surivive your cycle. Did they know when they sold them to you that you were putting them into a brand new tank, especially one with amazonia in it? I'd consider returning them to your LFS and finishing your cycle without putting their lives at risk.
1.0ppm ammonia is way too high when you have fish in the tank. Higher than .25 starts to stress them out.. they might be "alive" now but they won't be for long especially as your ammonia levels continue to climb (you're at 2ppm on day 3, I expect they'll get much higher within the next week).
If you want to keep them you may end up doing water changes daily - and I'd suggest doing more than 40%.. you need to get that ammonia down to under .25ppm, and that would be difficult with a normal fish-in cycle, nevermind adding a substrate into the mix that is also adding ammonia to the cycle.
Not necesarily true. Low ph and temperature renders ammonia relatively harmless....
Also you should be doing daily doses for prime. It detoxifies a large amount of ammonia.
I would take the cories out and put them in a spare tank with a sponge filter or something. They will be dandy there. Don't worry about it too much we all make mistakes. I did this recently as well. I thought I cycled it since ammonia was reading 0. Then when I did a water change at my new residence the next day it was 4ppm.