I don not have a solution yet and Shopify has been terrible and providing support for this. After many support tickets and chats I was able to determine that selling Apple considered my store as selling pseudo-pharmaceutical products which is against TOS so therefore, Apple Pay won't work. I am in the process of contacting Apple for support to see what steps I can take next. The Shopify admin has no useful system prompts of logging that provided any of this information so it was very frustrating and like pulling teeth with Shopify support. I will provide an update if I get one.