@urlreader
The IRS will always accept an amended return to pay tax you owe. The 3 year deadline is to claim an additional refund, if the change creates a refund. (But as noted, you are also past the statute of limitations.)
There are different contribution limits for a SIMPLE IRA, but that's something you have if you are self-employed, and is reported differently in Turbotax. The excess deferrals (from adding up the Code D amounts) should still have triggered the excess contribution situation even if you have other income.
