I have an older motor that needs to be replaced, it's got a 20" shaft. Have found a good used motor that is 25" shaft, can this be used and what are the risks? I assume that it may sit lower than the pontoons, slight angle issue? Thanks
Mmmm. Lots of horses.... In the early 80's, I had a 24 footer with a 140 and it would outrun everything on the lake.
I still don't think you'll have a problem. If you were happy with the old setup, I would try to raise the new motor close to the 5 inch difference and then lower it if you get any ventilation.
The only disadvantages of going too low are a little more parasitic drag and an increased chance of hitting underwater obstructions.