Also, when I went to the 'your shops' link ( https://subeta.net/user_shops.php ) it was telling me I had 0 out of 4 shops.

Do I need to remake my '!' shops and readd all the items into the new ones, or is there a way to fix my existing ones?

You'll need to create a new shop with the new system. These shops with a ! are legacy shops. You can take items out but cannot add anything in these shops and you cannot price items in there either.

New Shop Guides ^ Here is a handy link for you.

Please see above. I am going to go ahead and lock this up since it is not a bug.