I was thinking either file a 1040 with a schedule C for 16 & 17 and then a 1120S for 18 since it was approved for 18, or file a 1120 for 2016 & 2017 and a 1040X for the two years.  

The irs did not provide an explanation as to why the 2553 form was not allowed for 16 & 17 even though all steps were followed including the rev roc 2013-30 and the admission that the president neglected to file in a timely manner.

Any thoughts?

Your feedback is always greatly appreciated.