I tend to agree with Bill that it may be too late to make a late election for S corp.  Based on a plain reading of Rev. Proc. 2013-30, everything must be consistent with how records would have been kept and returns filed had the entity been an S corp from the effective date.  Also, and very importantly, the late election must be made by following the exact procedures prescribed in the Rev. Proc.  It is not clear, however, from your message that the election was made in this manner.

If you still believe that the failure was due to reasonable cause (e.g. because the taxpayer, who provided complete and accurate information to a competent tax adviser, had relied on the opinion in good faith to file the F.1040 with a Sch C), he may consider requesting relief by means of a PLR.

In the event you do take the route of PLR, I would make triple sure that the case is air-tight and review potentially contentious issues such as wages being reasonable before submitting the request as the IRS may scrutinize the details more closely than a regular filing.