Take a deep breath. Its not a race and everyone has a bit of a learning curve in this hobby, even old timers
Clown gobies are cute but they can be a pain in the butt to get feeding and love to hide out in the rock. Sometimes its just part of the acclimation, sometimes they're doomed from the start. A tiny fish like that will not cause an ammonia spike. If you're worried about it, do a few small water changes over the next week.
With a low bioload, you probably won't see much in your skimmer cup. Unless there is something in your tank that is producing something to skim, don't expect to see much. What kind of skimmer do you have?
Putting the boiled rock in may cause a mini spike (or it may not), however with little in your tank except for one fish, this would be the time to put it back in rather than waiting until your tank is full. Again, if you're worried, do several small waterchanges as you go. Likely you won't see a spike at all unless there is lots of stuff dying on the rock as it cycles.
With a 28G HQI tank I would imagine you won't really need all that much in the way of equipment for your tank depending on which way you go with corals. You're pretty much set. Just take it slow and try not to stress out over it. Eventually you'll settle in and wonder what the big deal was
