Is there a tolerance with Reg E when it comes to the interest you must give back to the customer to make them whole?

In order to make my customer whole I would owe them 1 penny.

If you owe them 1 penny - you owe them 1 penny. There are no regulatory tolerences.

Would I calculate the interest owed to the customer based on each transaction that day or the total of all transactions for the day?

If the total of unauthorized transactions was $1,000 and that amount was out of the account for 10 days, then it would be $1,000 x interest rate/365 x 10.

Essentially, the regulation requires you to make the customer whole. That means that you reconstruct the account history without the unauthorized transaction or after adjusting for an error. If the customer would have earned more interest, you must pay it. If the customer would have avoided a fee (any fee) imposed by your bank, you must refund it.