By going through your question I want to tell you that woocommerce will not use your custom template. It will use its own template.
As you want to use wordpress advanced custom fields plugin I want to tell you is that feature only works on the page and post. So as woocommerce will not allow to use your own custom template you can’t use advanced custom fields features.
Now just do something different. Just make your own custom template where you want to show your products. Then just go to the site http://docs.woothemes.com/document/woocommerce-shortcodes/
Here you can see the shortcodes for the woocommerce. Where you can easily show almost all products with your own customization. Now use these shortcodes to show the products. Here you have achieved that woocommerce is using your own custom template. Now as it is your own template you can easily use advanced custom fields with this. Is that clear? If any thing you can’t understand then reply me. Hope this will help you.