My ammonia went to just under .6 on my test kit pretty quickly and then barely went above that. My ph is 8.3, so acording to the test kit, 1.2 is fine and above that is bad. I wouldn't worry about your ammonia right now and if it doesn't move much, you're set. Once it started going down, I ordered the 2nd batch. Right at the 2 week mark.
You're in good shape so far. In my second batch, I got two tiger tail cucumbers. The boxes didn't make the flight (different thread) and when I got the boxes, one cuke had puked up it's guts. Gross. I put it in not realizing that it did that, and it moved a bit for a day and then no more. The other cuke was fine for about 5 days and just bit it. The ammonia still didn't go anywhere.
The rock has so much life on it that even if some of that stuff is dead, you probably don't have to worry about it. Of course, if you know it's dead, get it out of there.
Just added two clown fish (Nemo's) and a finger leather on Thursday. Everything is happy.
-Brendan