Presumably the Form 1099-R that you added in step 3 was the same as the Form 1099-R that you removed in step 1, with the same answers to TurboTax's follow-up questions to entering that Form 1099-R, so the only relevant changes were the addition of the traditional IRA contribution and the correction of the Roth IRA contribution.
The resulting $56 refund from the amendment sounds a higher that expected, but possibly correct. Reporting the traditional IRA contribution should have reduced your AGI by $196, reducing income tax by $24 for income in the 12% tax bracket. Perhaps the reduction in AGI also moved $196 of qualified dividends or long-term capital gains from being taxed at 15% to being taxed at 0% instead. That would probably entirely explain the refund amount.
