Do to email issues a customer was unable to getthe CD on the third business day prior to closing. The borrowers contract expires and the seller has their purchase scheduled following this closing. Not closing on this date could cause financial issues. Would this qualify for a waiver?

Waiver of the three day waiting period is like waiving the right of rescission. Bank decision as to whether to accept.

Were the email issues on the customer's end? If the Bank can document that it "delivered" the disclosure under a compliant E-SIGN process, would that not satisfy the requirements? Not saying I would be completely comfortable with the situation, just throwing the thought out there.

Yes we use a secure portal and the customer got the email but could not get logged in to view it

If they had previous went through the E-Sign demonstrable consent handshake, if they don't actually open the document, then deliver and the closing date would be based on the 3+3 day rule.