If you don't have the employee's signature agreeing to the "tool deduction" on his paycheques, then you're probably already in violation of the FLSA. Given this, you have two options:
1. Deduct the balance owing for the tools from his final pay. Your risk is that he'll go to the DOL and complain that this big deduction wasn't authorized by him. You can try the defense that he seemed to agree to all the smaller deductions because he never complained about them, and because he quit, you had to make the remaining smaller deductions all at once. This may or may not fly with the DOL. If it doesn't, you will be ordered to pay back to the employee all the tool deductions - the small ones + the big one at the end. You will then be free to sue him for the entire amount in small claims court.
2. Pay him his final pay and sue him in small claims court for the balance due for the tools. He may still go to the DOL looking for the smaller deductions, and if he does, you will be ordered to repay him all of those smaller amounts. You will then have to sue him again for the smaller amounts.
Lesson to be learned from all this: Never lend employees money, for tools or any other reason. If you do lend them money anyway, make sure you have them sign an ironclad contract that lays out repayment terms (and penalties for not meeting said terms). The signing must occur before the lending. A competent attorney can draft up an ironclad contract template for you, and this will be worth the cost to you so that you can avoid having to go through the hassles described in numbers 1 and 2 above.