You can also go ahead and file the tax returns using form 8919 to report the income as wages and to shift the employer share of the social security and medicare taxes back to the employer. You can then use form 2106 and Schedule A to deduction any unreimbursed job related expenses.
However, that won't necessarily produce the best results, depending on the level of expenses that you had. Therefore you should run it both ways. (Schedule C vs filing an SS-8 and then using forms 8919, 2106 and Schedule A).

