I am new to mud motors, however I have been having a weldbilt with 18 inch sides and 16 inch transom for some time. Well I am a full time college student and after saving money for some times I finally bought a 36 horse pro drive long shaft. Well the motor is on my boat, is sitting high in the water, and only treading 4 inches of water with no one in it. However, this weekend I am installing a 6inch set back jack plate with 6 inch vertical adjustments to reach the 19.5 transom height required for the motor. My concern is once I install the jack plate (only weights 15lbs) is that if the 6 inch setback due to the leverage increase makes the boats transom sit lower in water to where its too low. any help is appreciated and maybe some one could inform me how much transom should be sticking above the water.

If it was me and wanting to do it on the cheap, I would sandwich a piece of aluminum 4" high by whatever thickness your transom is between two pieces of 3/16 or 1/4 aluminum and have it welded. Slip this over your existing transom and secure it with bolts or weld. The wider you go will help also.
something like this flipped 180
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Don't build a jack plate that sets the motor back off of the transom, bring your boat get the transom built up to a tall transom and run it like that. Pushing the motor back will move more weight to the back of your boat and cause it to squat more in the back.

Did this on all the Jon boats we put Mud Motors on, never had an issue with any of them.