If you don't have a copy of your W-2 (and can't obtain one from your employer online), you can paper-file with a Substitute W-2.
If you are reporting 1099-Misc income and only see the last four digits of the EIN, you can report this income as 'Other Income Not Reported on a W-2 or 1099-Misc'.
Go to Deductions & Credits and scroll all the way down the topic listing to Less Common Income > Miscellaneous Income 1099-A, 1099-C to get there.
You could then mail your return with a copy of the Wage/Income Transcript attached.
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