My initial guess would be gill flukes, so yes a parasite. I'd probably start by separating him and placing him into a QT tank, with salt at 1 TBSP/10 gal for stress.
My concern is that you're getting large ammonia reading each day, this would be highly toxic and highly stressful for your fish. Did you not seed your new filters with media from the old HOB? I'd be looking into using praziquantel for the suspected parasite, but I'd wait until someone more experienced chimes in. For now, just isolate him and add the salt to reduce the stress on him