1.will a 40 breeder be ok for him?
Should be fine, especially if just a temporary situation. I've also kept juvi boas in tub set ups like we do for BPs
2. Im going to use paper towels to start since I want him quarantined to make sure no mites. Is this ok?
Yes that is fine.
3. What kind of hide or other stuff needs to be in the tank. Obviously he will have a water dish.
Hide and water dish. If you want to provide something to climb on, go for it, but when in QT, best to keep minimal. 2 hides if you have the room.
4. Any other tips you can give me.
Boas are pretty hardy and easy to care for. They don't need to feed as often as BPs. They can be very foody and stay in food mode for up to an hour after feeding sometimes.
I'm sure you'll do great!