Sounds like a heavy bioload for a 55 unless all of your fish are small.
What species of puffer and lionfish are you referring to? Puffers and lions often make poor tankmates as puffers can't seem to keep their mouths off of lionfishes' long, pretty fins.
Since your fish is gilling and shedding its cuticle, it sounds like it's infested with either flukes or ******. Cuticle shedding is normal, however, excessive cuticle shedding is the fish's attempt to rid itself of ectoparasites. If it were ammonia poisoning, I suspect all of your fish would be affected. Labored breathing isn't always associated with ammonia poisoning.
Does the fish have spots? Look at its median and caudal fins to see them the easiest.
How long have you had the lionfish, and did you QT it? If so, for how long?
What are your water parameters? (temp, pH, ammonia, nitrite, nitrates as a minimum, and "fine" is not the answer we need to see to help you diagnose your troubles).
As for krill, ESPECIALLY freeze-dried krill, as mentioned that's about as poor of a diet as you can feed your fish. Even worse, krill has been linked to lockjaw in many predatory species, esp. lionfish. Additionally, many fish refuse to take any other foods once they becom "hooked" on "fish crack" (as FD krill is often referred to).
A couple of pics of your fish's condition would be very helpful here...
If you're really serious about keeping a lionfish, I highly recommend giving our lionfish care article a read:
http://www.lionfishlair.com/careguides/lionfish.shtml
I also recommend taking a peek at our weaning article:
http://www.lionfishlair.com/feedingtechniques/toolsofthetrade.shtml which will give you a lot of info on weaning your fish and the types of foods you should consider.
If you need them, we also have an article on understanding and treating ****** (ich) as well as a QT article...just LMK if you'd like links.