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I was on a tight schedule and my mortgage guy told me that a copy of my tax return AND independent verification which in my case was a copy of the cancelled IRS balance due check from the bank would suffice. Most mortgage people know that there is a several month delay between filing and availability through the 4506 and they have alternatives. Good luck.
The online access to transcripts is tooooo slow for the usual mortage process. I simply wnet to my local IRS office and has a service rep there print the transcripts for me. Submitted them to my lender and the file was cleared and closed. I recommend that you do the same.
Yes, the tax advocate is there to help you. Espeically if its causing some sort of hardship for you and your family. Make an appointment and go see them in person if all possble.