metal repairs are subdue made with "marine tex".there are several marine sealants thatserve as glue and sealant. check your native marine store.

This is what i utilized in my old aluminium boat. on the inside of the hull where it was covered and no one was going to walk i used 3m automotive body undercoating. it worked very well. now since you are replacing the transom i would dissemination the undercoat on the inside and use a good marine grade sealent on the outside where the bolts go through. the reason i employed the underbody coating is that it doesnt harden up and flexes with the boat hull.

The 3M stiff sealant is actually called SEAM SEALER

The same thing you see in the back of pickup trucks covering the bedsides custom-made to the bottom side.

It does not harden but stays in place - keeps out water, and it will last forever.

It comes in a caulking gun tube and is clear to work with.
Also paintable.

5200 aquatic sealant home depot is the best price sure mineral spirits as clean up. It is dishwater cure so if you are putting it in a area that's air tight like metal to metal spray a cheap mist of water or it Will not cure.Hope you don't have to take it apart.I have also use nail it exterior waterproof adhesive it's less well-to-do an holds great.

all boats are other -- the jon boat however is easy to repair -- you should use some heavy-duty right angle brackets to re-invest a new wood transom --- cut and shape the wood for a near ''o'' tolerance to fit the rear of the boat -- go to the ''mucilage section'' of Lowe's or home depot and find a product of two-part epoxy to seal the wood to the metal --- if applied too heavily it's okay because when dried you can stain over and it will look fine also the rivets are a two man job --- try to hold the rivet head with the side of a shop hammer (use like an anvil) and tap the smashed end of the rivet tighter _---- after tightening the rivets use the epoxy to seal the old rivets to the propitious floor of the boat --- this will also cause the boat to run quieter and decrease the leaks -- alot of bolt holes in the transom can be unchangeable with the replaced new wood --- the size of the motor is a factor to consider,,, the larger the horse-power the stronger the transom must be to restrain the pressure of the motor pushing the boat thru the water...