If I can give you some advice...NEVER offer such absurd discounts on your time. Always charge what you are worth. Otherwise you will get people who will not only waste your time but try to stiff you on the (meager) bill. You could not get me to look at a project like this for less than 6 BTC/hour.
I think my advice/suggestion is a contract for the whole project/job. Ask for full charge instead of paying per hour. With pay per hour, you would face problems like this current one. Some will charge you for just looking at your code and claiming they lost time and that their time is money.
Yes, a flat rate for the job is reasonable if it's short and obvious and nothing goes wrong. Installing a shopping cart probably qualifies. Making it work with Bitcoin probably doesn't.
"Typical time to set up the cart software(getting it onto the server, setting up mysql,etc) typicaly runs 2 hours."
I just don't see where the hours went. It's like, pre-made software, and the pluging module takes all of a moment to install.
And how is it his fault that MyBitcoin decides to go offline? It's starting to look to me like you just don't want to pay your bills.