Then from a strictly regulatory viewpoint, I'm afraid the consumer has properly asserted a Billing Error and you can't rebill. You might be able to hold him liable for the $50 the reg allows (that's per fraud event, not per transaction) assuming it is disclosed in the card agreement. One caveat - if the transactions in question are not ATMs, then you are not allowed to bill anything thanks to the association's Zero Liability policy. If they are ATMs, the policy doesn't apply.
What you can do is provide the documentation to the consumer and ask him to explain it - you are sending this documentation to him and would like to know what he thinks about it. Don't address the fact you got this from an investigation and took too long or that you want to rebill him, let him draw that conclusion and accept the transaction as valid. Once he withdraws the dispute, you can then rebill him.
However, if he doesn't want to withdraw, you're stuck with it. Sorry, but the rules require you to make a timely investigation.