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@CUSO wrote:

 he did not set up any payroll (though he should have). 

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Did he not set up payroll?  Or did he not take compensation?  They can be very different.

I'm rather unpopular with my opinion, but ...

If he took money out of the corporation for personal use, it is wages and/or distributions.  Unless he specifically tells you all of that money is non-wage distributions (and the fact there is a SEP indicates that is NOT the case), he DID take wages/compensation, but neglected to file payroll forms.  That means the payroll forms should be filed now.