I think either Titebond or Gorilla Glue will work. Titebond is as waterproof (or more) as the glue used in exterior plywood. Gorilla Glue us urethane-based, I believe, and it is also waterproof. Gorilla Glue needs some moisture to cure; I don't believe Titebond III does. I found Titebond to be much easier to work with than Gorilla Glue.
The bass buggy, isn't a little toon with an OB pod on the back? Man post a pic of the whole set up, I'm curious what your boat looks like and what size motor do you have for it?
So I used gorilla glue last night...so far so good..but now I'm wondering...can I use this (or the titebond 3 which is probably easier to spread) to seal up the outside and edges?
I'd use something that penetrates and/or encapsulates the wood better. Woodonglass advocates the use of some stuff he calls Old Timers' Formula... this would probably be a good candidate for sealing the wood.
Good stuff for sure but... You see the size of the transom? Not sure they sell all the ingredients in the amount he would need.
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Do your test fit, drill mounting holes and when all is well seal the new transom with spar urethane gloss, you can get it at Home Depot. Since your transom is small 1qt would more be more than enough for 3 coats on the flat which would be like 6 on the edges.