File a lawsuit. You would sue the employer for the amount which is your best guess by which you were unpaid (including having money withheld from when it should not have been). In the lawsuit, your employer will have the chance to justify the amount you were paid and may be able to prove to the court that you are mistaken and you were paid correctly--but if he can't, and the court believes that you were underpaid, the court will order that the balance be paid to you. If the amount of money at stake is less than or equal to the limit for small claims court, suing in small claims, as your own attorney ("pro se") is a very good option. Good luck.
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