I remember those previous posts on this issue, and it still amazes me now. This stores business is satisfying customers with their products. At $6k, they can't afford not to have happy campers, or disputes at that.
It seems to me however that somehow they've got there wires crossed and have done all the wrong things in dealing with this situation. Perhaps you should head down there in person and ask to speak with the manager again to see if you guys can come to an understanding. Theres no saying the manager will even see you, but just remember to make them feel comfortable, and perhaps he will. Explain to him what you've explained to us. You want to pay for what you've got, and recieve credit for what they've failed to supply. You would prefer that this issue be resolved amicably, and not through legal actions.
You need not explain to them that this is in their best interests as well, bad press and bad experiences have a way of circulating and a way of ruining stores. Any patronizing on your behalf will only make this farce worse. This is something they should want to resolve just as much as you, and if they are not willing to meet you on this issue then were I you, I would have no problems in burning this bridge and maintain the status quo with the CC company and further push the dispute.
Mind you, I'm not really a nice person.
Good luck