I found some of my dad's old wooden Bossa B's. I think I'm going to repaint them and put new hooks. Anyone have any information on the best paint to use on old wooden baits, or any information that would be helpful?

Do you mean Balsa B's made by Bagley?   If you really want to fish those baits then I would suggest you send them to somebody that has experience at refinishing a wood bait.   To do it properly the old finish needs to be removed( I do it with a propane torch) then the bait needs to be sealed, primed, painted, and clear coat.   

The quick way would be to scuff the old finish, prime, paint and then clear coat.   But if those were my baits I would invest the cash to have it done correctly.   

If you decide to tackle the project yourself, keep asking questions right here, you will get all the answers you need.