Do I have to clear all the EF Messages before I can e-file an extension?
No, only those messages on the ETD_MSG page must be cleared to transmit the extension by itself. These messages are related to the extension not the actual return, and must be cleared before it can be transmitted.
Any regular MESSAGES page refers to the return itself and may be produced because the return is not finished. These will not prevent the extension from being eligible for e-filing.
Business returns: You may see a Messages page (EF Message 0147 or 0148) stating that the extension has been previously e-filed and accepted by the IRS, and that only the extension will be prevented from e-filing.