You should not do the amendment until your tax return is fully processed and you receive your refund. Don't spend it all though, because you will probably have to pay a 1/3 of the ordinary tax from the 401K withdrawal when you file the amendment. The 1040X won't be ready until late next month anyway. If you pay back the amount you withdrew within the 3 year period, you will be refunded the taxes. But not until it has been fully repaid.
Oh, and this year, you will be able to e-file the 1040X, so that should make it easy peasy!
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