I would switch lenders
I can understand the lender wanting to verify your tax return with the IRS. But you would think they could waive that requirement for minor discepancies. With all the new HUD requirements maybe they can't. It's worth a few phone calls to other lenders to see if they have the same requirement.
The lender can also get an "official" wage and income report directly from the IRS. This report is a transcipt of every W-2 and 1099 you received for the year. The wage and income report should agree with your amended return. Any tax preparer registered for E-Services can get a copy of this same report for you online in about 30 minutes.