I'm sorry for loss. It sucks when classic gear gets destroyed by a hurricane like that. Didn't the owner know to get out of town, and to take his most valuable possessions (like a BFSR) with him to a safe place?!? Just kidding, of course.
I would not have second thoughts about a Mojo birch ply baffle. That's the best material you can build a baffle out of, and Mojo does great work. In the big scheme of things, I wouldn't pause to think about how the baffle might change the tone of the amp. If the speakers got wet and are being replaced, THAT is where your tone change is going to come from. It's not like any finicky musician could blame you for the baffle changing the tone when he had to replace waterlogged speakers. If he's not happy with the tone, then blame Irma.
AFAIK everyone in their right minds made baffles out of plywood, not solid pine. Back in the day cabs were made out of pine boards, baffles were made out of plywood. Eventually both came to be replaced by MDF.