When you're entering these sales into TurboTax make sure to say "I'll type them in myself" instead of importing the 1099s from your broker. Then enter each sale as it should be - noncovered with the correct acquisition dates and the correct basis as you have it in your records. The sales should show as they actually were even though those figures and dates are not correctly represented on the forms that you received.
At that point you have two choices - you can submit the return as is and save all of the proof that you have so that if the IRS asks later then you can prove the transactions were as you entered them. Or you can mail in the return along with copies of the proof that you have (never send originals) so that the IRS already has everything. I usually just say wait til they ask but some folks don't like the waiting for something that may never come.
@Jhenn
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