I am a newbie, basically, at least to the saltwater side of this hobby and my first purchase of fish after a couple damsels that I had used to 'test' my tank's cycling (which are a b!#$@ to catch, by the way) were two clown fish and a porcupine puffer. I got all four fish from the same tank at the same LFS and I put the clowns in about two or three days ahead of the puffer (just had him on layaway). My logical thinking, coupled with a few marine compatability charts, led me to believe this was all going to be ok. Well, the two clowns died about two days after I put in the puffer, but I thought it was a rock slide or something that killed them and got two more clowns...keep in mind in my area, they are about 15 dollars (US) each. Needless to say, they had the same fate.
I struggled and struggled with the puffer issue since this was actually my wife's fish (I got the tank, she gets her fish sort of deal) I couldnt just trade him in. I went the same direction as many people and bought a lionfish and a snowflake moray eel.
This set up worked fine and if I did not get so bored at looking at an empty tank all day, I would still have these fish. The problem wasnt so much anything I could really see, but at night time was when the puffer got excited and it would even try to 'nip' at me when I came downstairs and turned on the living room lights.
So, a couple days ago, I decided that I would take all three fish in for store credit. This puffer never did kill the lionfish, but I saw some similar things as you did with the apparent bite marks and nipped fins. My assumption was always that the puffer would eventually get stung if it didnt quit being a bully, but I guess it was smart enough to stay away.
Anyways, my point is that with a puffer, things become seriously deminished when trying to stock or restock. I wouldnt say that it is impossible, because I do not know that, but my little puffer, about 5 inches also, would not let me even put a snail in the tank, regardless of how huge I bought it. I have seen a very large, almost full grown puffer though, and I am telling you, I would seriously think about buying it if it didnt cost about five hundred dollars. They are awesome fish and have great personalities, but they often times turn on tankmates with really no warning to us. I really feel bad about your situation and just wanted to let you know that you are not the only one who has gone through this. Keep your chin up though and research every possibility before making a complete decision. Good luck to ya!
I think I am going to have to get rid of my puffer, or I won't be ableto get anything he won't kill. 
