Xstlhdr,
When your motor is mounted at the proper hight,the part of your shoe that is closest to the boat should be 1/4 - 1/2" below th bottom of the boat. Transon hieght is all irrelevant until you accomplish this. And the trasom angle of a Jon boat is a little less than a big alum sled, so I would go with 1/2" or it will cavitate alot.