I have some trouble navigating your site and seeing the categories_id due to your url rewrites ...

Are your sure all Products that are Kits have the master_categories_id of 316?

And you appear to have installed Flat Rate, but before you said you wanted to use Item Rate as the charge for Products in the categories_id 316 ...

Flat Rate flat is a static charge regardless of the number of items in the cart and Item Rate item is to charge an specific charge per item in the cart ... which are you really meaning?

You had said at the start, you wanted:
Example: All Operation Homebrew beer kits ship for just 5.99 each!! Choose 1 kit, it ships for 5.99; choose 2 kits, they ship for 11.98...