If the IRS wrote a formal letter to you, instructing you to file 2006 and 2007 tax returns (common for taxpayers who need to catch up with the IRS to settle prior years before the current year can be done or a payment plan agreed to), then you have to file those returns.
It's possible that there are no transcripts because you never filed any returns for those years, although my recollection is that transcripts by mail go back only 10 years or so (online is much less).
You have to do as best as you can, on old paper forms. If you can't do it quickly, by all means reply to the IRS letter, explaining your difficulties. The worst thing in the world is to break off communications with the IRS.
