Is there a way to change the font color and size in the area where you would put the choices so the customer can't complain that they did not see the options. Sometimes when you order on line you do not look at the entire form so if you could change the location & color on the form for the shipping information it might make it a little more noticeable and hopefully it might make life a little easier for you. It sounds like you are really trying to be fair but you also have to think of yourself staying in business.
Just my idea for a tricky situation. Good Luck with what ever you decide to do. It is nice to hear there are still small shop owners trying hard to give everyone great customer service.