I've never had my LBS charge me the shipping for something I had ordered. I wouldn't pay it, especially since the order is a week late.
I can't believe you actually supported them and lost a lot of money on the deal when you could have saved money and got the same order on time through an online store. I say forget about them and order it online and don't go back there. I'm sure there are better LBS stores in your area you can get to.
Koffee