Jon boat transom

I have a 16 ft. flat bottom jon boat that the plywood transom is rotting away on. In the future i would like to put a 25 to 40 horse outboard on and was thinking this would be a good time to change the height of the transom. The boat has a 16 in. transom height now, is there a standard height for outboards in this horse power range? I know if i buy a new outboard that you can get the correct shaft length for my current transom. Can you find a good used outboard for that 16 in. transom.
please help!

Most of the time you have two basic sizes, short shaft (15") and long shaft (20"). Ive seen short shaft transoms be 15-16" and long shaft 20-21". You have a little bit of adjustment when you bolt on the motor. Just make sure youre cavitation plate is level with the bottom of the hull and you should be good.

Because the transom is on an angle it'll usually measure 16" but if you measure at a right angle to the bottom of the boat you'll find it's closer to if not exactly 15". Taking an existing 15" transom and making it 20" usually involves some metal work plus often times the knee braces are taller on a 20" transom. Jack plates take this into account by the way they fit over the existing transom putting the pressure back down close to the knee braces, just adding more wood doesn't and now the force against the transom is 5" higher or 5" higher above the knee brace which can cause the transom to warp or even break off on top.