This is a real problem for you.
Lender can not close until they have comared your tax returns provided against your transcript.
If you filed an extension, these transcripts are taking more time than usual (4-6 weeks around April 15th) and just got your taxes in, it could take 8-10 weeks.
You may want to go to the local IRS office and request a copy of what they have for you. They will stamp it with their own (antiquated) stamp and the underwriter will recognize it as coming directly from IRS. This may work.
This became such a problem for us, that we now request 4506T from the inception of the loan (right after disclosures).