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To review...you filed a 2006 tax return without entering your W-2 information, and neither the IRS nor the Social Security Administration has any record of your earnings for that W-2.  You say you earned $48K and paid taxes on it.  Can you contact the former employer to get some verification from the employer?
Did you just talk to "someone" at the SS office or did you actually try making the written request to SS for that W-2?
Have you tried requesting a wage and income transcript from the IRS? They can provide a transcript for up to 10 prior years--you are kind of on the edge.
 <a rel="nofollow" target="_blank" href="https://www.irs.gov/individuals/get-transcript">https://www.irs.gov/individuals/get-transcript</a>
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