Yes, that is accurate you will have a penalty for 2012 and 2013. For 2012 it should be $750 (6% of $12,500) and for 2013 $360 (6% of $6,000). In 2014 the excess will be absorbed and you won't have a penalty on Form 5329.
Yes, you will have the 6% penalty on line 9 for Form 1040-X for 2012 and 2013.
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