I have a customer wanting to change the product and then pay the difference. Is there any way to accomplish this?

1. Change the customer's order on the Edit Order screen. You'll want to be very sure that you're adding the correct product at that point, because you'll be editing the raw data of the order. That is, the system won't stop you from doing anything there - you could add $10,000 worth of products to the customer's order and the system won't care.

 
2. On the orders dashboard, add an additional payment for the order to bring the total up to what it should be. The system does not store customer's credit card number, so you will need to call the customer to get their payment information over the phone.

The alternative is to simply cancel the customer's order and refund their payment, and then ask them to order the item they really wanted. That's simpler, but of course you risk the possibility that the customer will change his mind and not make the new order.