Just to let everyone know this was a simple fix once I thought about it properly LOL

Code:
To list only in-stock products, open includes/languages/english/extra_datafiles/your_template/best_sellers.php
set BEST_SELLERS_SHOW_OUT_OF_STOCK to false
My store is all downloadable products so I have the stock count disabled, I set it to true in this file and there they all appeared LOL :)