Hrm, missed this post.
It sure did sound like perhaps your tank had poor water quality. Almost sounds like your bala shark got ammonia posioning (from what you describe about the gills). I know its a bit late now, but what sort of setup do you have? In all honestly, I don't think LFS should sell bala sharks to begin with. They need large (read as very large) tanks with tons of swimming space, and grow to be quite large as well and generally do better in schools of 3 or more. I've heard quite a few stories of how someone accidently spooked their shark, and it ran head first into the side of the tank at full speed.... not very fun.
Hope you find the cause of your sharks death... please don't give up, FW systems can have their fair share of fun too.
-Rich
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