I agree with you re: preparing the 1040 first .  Lesson learned.

Income was not double reported.  What I know is that some 1099's were issued to her SS and some (different from the SS ones) to her Sole Prop EIN when they shouldn't have been.  

I'm doubting that she issued a letter on corporate letterhead.  She's not honoring the purpose of the corporation.  I realize that and am trying to clean this up for her so she can move forward.  She doesn't want the complications of managing a C corp and would like to dissolve the corp and go back to sole prop or single member LLC.

Yes, she is using her personal car for business and letting the corporation pay for all the operating costs.  

Thank you for all your input.  It's appreciated!