Hi deckcakes.
No expert here but hopefully I can help. And there's no such thing as a dumb question. Not long winded at all... you've given lots of details... that's a good thing. I think I'm the queen of long winded posts. lol Now stop pullin' your hair out and tell me if you've tried this yet.
From what you've said, all I can figure is that you need to update your store categories. If you haven't done this, go to My Account, eBay Settings and Update Store Categories. Then when you create a listing, check the Store Item button at the top (which you obviously know), and the category options appear in a drop down below the main category boxes.
When you change your categories on eBay, they'll need to be updated on here this same way.
I hope this gets you going with it. Let us know please?