It would be to your advantageous to find another local tax professional as a 'mentor' for things like this. Seriously, if you are preparing corporate returns, you need to be very familiar with them or have somebody to assist you and review them with you.
Here are a few of the potential issues I see:
1) You mentioned a "late S-corp conversion". Do you mean you are NOW electing the S-corp status, or that the election was timely filed, and the tax return is just being filed late? It does not qualify for the late election, as it must have been treated as a S-corporation, which would include payroll.
2) Yes, some tax preparers put the compensation on Schedule C. They are also signing false tax returns. That is not correct, and you would be signing a false tax return if you do that.
3) If the vehicle was not contributed to the corporation, it doesn't go on the corporate tax return. It can't deduct expenses for something it doesn't own. If there was an Accountable Plan and the shareholder submitted timely reimbursement reports to the corporation (minimum of every 60 days), the corporation could deduct the reimbursements. Otherwise, it is an Employee expense on Schedule A, subject to the 2% limitation (and subject to the amount of W-2 wages for that business).
4) Corporations do not qualify to use the Standard Mileage Rate.
