If the bank receives a "search and seizure warrant" and there is funds in the account above the warrant, can the bank charge a fee for processing as we would if it was a garnishment or levy

It would depend on the law under which the search and seizure warrant was issued.

Also what can you tell the customer when you take all their money out of their account. Can you give them the agent's money or tell them about the warrant? What can you say to the customer.

Talk to your attorney.

Correction, Agent's Telephone number?

that is a question you should be posing to bank counsel...could have both state and federal implications depending on who issued the warrant