We have a custom record that manages customer input / actions. We send automated emails when the the action has been resolved (this is different than our Customer Support). Anyways, if a customer responds to the email in the custom record, we arent seeing any sort of event on the netsuite side where we can "open" the input automatically via workflow or script. Any suggestions?

How about using the Email Capture Plugin? I assume you have control over the sender & recipients of the emails sent from the custom record.