Hello, recently I have upgraded the motor on my Jon boat from a 2.3 Honda 4 stroke, to a 9.9 Yamaha 4 stroke. Although there are a plethora of benefits from switching, I have found so far only one dilemma; that being It's a long shaft. One of my main reasons to buy a Jon boat was to have the benefit of cruising into the shallow waters that I fish. With a long shaft that isn't even possible to conceive. Being of no income at this time, I am planning to build a jack plate here shortly without the extensive use of welding. While thinking (Lets be honest, daydreaming) about this at school about a week ago I came to the cold truth that building a variable height plate would be to difficult and require a great deal of welding. So my question to you is- Where should my prop (or the main fin just above the prop) be in correlation to the bottom of my boat as a general standard? I want to be able to get the best performance out of it as well but just don't know how high is too high or too low is too low. Any help would be appreciated.

The rule of thumb used to be that the anti-ventilation, once known as the cavitation plate, should be level with the bottom of the boat.  However, in this day and age of jack plates, set backs, etc., this old school practice has become obsolete in some cases.

 

However, the old school rule of thumb is still a good starting point.  From there you can adjust it up, or down to determine what works best for you.  The ideal height will vary depending on load, and load distribution, water depth in the shallows you will be negotiating, etc.

 

All you need to do is to make a jack plate that will raise the motor the difference between the two motors.  If your current shaft is five inches longer, raise the motor five inches, and adjust from there.

On a Jon boat, I would not try to ad any set back. If you are using a long shaft motor on a short transom. You will need to add at least 5" to the transom height. As mentioned, with the motor sitting on the boat, measure from the bottom of the hull to the anti-cav plate and that will give you the the height you need to add to the transom.

A couple pieces of 1 1/2"x 2 1/2"x 1/8" angle will make you a plate to raise it. A couple vertice pieces bolted to the boat and a couple short horizontal pieces welded to them and a short piece of 2x6 in them and you have a mount. They used to sell mounts just for what you are wanting to do.

Here's one BPS sells http://t.basspro.com/MiniJacker-for-Clampon-Outboards/product/8782/?URL=http%3A%2F%2Fwww.basspro.com%2FMiniJacker-for-Clampon-Outboards%2Fproduct%2F8782%2F122143&hvarAID=vantage

I think I will make something out of the angle like you said and make the plate the motor mounts to out of corian.  Once I finish it I'll post how it turned out.