Can you file a shortage for per diem on your taxes? If so, what basis is used to determine that difference?

Yes, if per diem paid by employer is less than the reimbursable per diem, you can claim the difference as itemized deduction on schedule A (Form 1040). This is employee business expenses which are subject to 2% AGI deduction.

Do you base the difference from your state's per diem rate or federal per diem rate?