Transition from Subdomain to Primary with GoDaddy and now issues?

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So, a customer was using a Domain provided by GoDaddy and used a subdomain for the shopify store as they had a GoDaddy store they wanted to keep up.  Whenever we transitioned the store and products from the GoDaddy site to the Shopify site we then closed the GoDaddy site and transitioned the Shopify store from the subdomain of to the primary 

Since then we have experienced issues from users new and old, after visiting the site. (Again never had a issue reported prior to the domain switch.) Most of the issues revolve around the cart or checkout process including not being able to remove the items from the cart. Another issue has been the completion of the checkout would hang not creating the notification email that an order has been placed, but still completing the order process.  This left users in a hung state on their screen and they would call to verify their order had indeed been processed and we received it.  

The site doesn't use any app for processing orders or any app on the cart.  The only edited code resides on the website in places to prevent un-registered users from visiting products and parts of the website which is only accessible to verified accounts.  Also this code was in place prior to users experiencing this issue.  Support mentioned they would be able to troubleshoot if we loaded an unedited theme, but I still wanted to check with the community to see if anyone else had seen this issue.  Wanting to avoid a prolonged downtime as we would have to close the online store while support conducted their troubleshooting on the issue.