The shipping quote value that you see is not based on the number of items in the cart but rather the total weight of the cart. This is done on the confirm pages, in the server behaviors it is passing the total weight for the cart.
As for editing the advanced options the links you see are correct, but clicking on them should bring up the interfaces for editing or deleting the option. I'm including some screen shots of this for reference.
Are you able to get to the edit or delete interface with any items options? What are the name and values for the current options you are working with?
