it does look like the ammonia may have been the culprit and yes the black is the healing from the burns. the spots on his gills sound like breeding tubercles and indicate that your fish is a male. as he seems to be getting better then just watch him closely.
if you ever have to catch him then have a net and a wet towel or face cloth handy. once caught you can wrap him in the towel and then use a finger to gently lift the gill flap to have a look. as the fish wont be too happy to be out of water then have someone to help you and hold him over the pool in case he manages to slip free.
im not a fan of ammolock as yes it does disguise the real readings but as long as your aware of that then thats fine.
if the filter is new then it will be going through a cycle and the ammonia may increase and then turn to nitrites.
keep testing your water for any signs and do water changes if anything climbs.

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