I wouldn't be so quick to discard velvet after the examination of one dead fish. Many parasites leave a dead fish. Cryptocaryon needs a bit of time to leave since it in inside the skin. Amyloodinium just needs to retract it's "straw" and is off to "greener pastures".
Another difference is that Cryptocaryon has to encyst to get to another fish even if it hast to leave early. Amyloodinium, if less than 24 h on the host, can leave one fish and directly infect another.
The only way to be sure would be a live biopsy of the gills (if you have the guts for that).
Another thing: I have never seen fish breathe heavy due to an occult or visible low level Cryptocaryon infection. Usually an ich infection needs to be pretty progressed to cause rapid breathing.
Amyloodinium on the other hand usually starts with affecting the respiratory system heavily before showing on the skin.
I would give these fish a prophylactic freshwater or formalin bath to dislodge eventually present Amyloodinium. If the fish have velvet you should find something in the bath water (maybe strain it to a sufficiently fine micro sieve).