As of now I have a Aluminum jon boat. I have a 36 ld thrust motor. I can get a 16 Ft fiberglass V boat for free. Now will this motor be able to push the boat.  I would get a small gas motor for this as well.  Just need to see if it's worth it.

If you are going to get small gas motor then i don't see why it wouldn' be worth it.

Now, if there are a lot of things wrong with it, like the floor, the transom, the hull, anything like that, then i would simply put the small gas motor on your aluminum boat and call it a day.

If this is a fiberglass boat with decks I'd say you're 36lber will perform rather unsatisfactory, at least compared to what you've been using it on.