Outboard mounting height?

I know this has been beat to death, but I have a few questions regarding my specific setup. I have a MonArk 1644 with a 20" transom. My motor is a long shaft Mercury 25. My motor is pulling my boat to the right. It was much worse until I moved the skeg/anode as far to the right as it would go. It helped quite a bit, but it still pulls. I have water shooting up the back of my transom. At certain speeds quite a bit of it is going over the transom into the boat. I measured my cavitation plate, and it is 3" below the bottom of the hull. Performance is reallly not an issue, in regards to speed. She is a screamer! Light loaded she will run 30mph. Could all of these issues be related to the motor being mounted too low? Thanks!

No, all of your issues are not related to the mount height. That being said, you are giving away performance and fuel effiency by having your cav plate that far beneath the boat. Raise the engine!
As far as pulling hard one way or another beyond what the trim tab will give you..... change tilt angle. Move your tilt pin and run the boat again. With each tilt pin move you will feel the torque steering either get worse or get better, this will tell you which way you need to go with the tilt angle.
There is an effect in aircraft called "P-factor" or propeller factor that has the same effect on a boat using an outboard. Physics is physics after all.
In your head picture a transom that is straight up and down (yours is probably around 15 degrees negative already) and an outboard that is straight up and down. Now visualize the propeller....all blades perfectly in line in a vertical plane. Now tuck the engine under......the lower blades are the leading blades now, right? This will produce a steering torque effect in one direction. Now visualize the engine tilted out and the upper blades are the leading blades. This will produce steering torque in an opposite direction. Understand?
The reason why is that the upper blade is moving in an opposite direction than the lower blade is moving (don't think clockwise or counter-clockwise just think right and left) when viewed from either straight in front of or directly behind the prop, therefore steering torque is affected by the angle of the propshaft.
As a kid a spinning Top always wants to straighten itself up, corrrect?
By far this is easiest to feel in a boat that has a mechanical steering cable and tilt and trim. While on plane and at a steady RPM trim the engine up and down while feeling the steering torque change from pulling one way to pulling the opposite way.
In aircraft, specially tail draggers, the lower propeller blade is always the leading blade and produces quite alot of steering torque during take-off until the tail comes up. You have to be ready for this torque or your aircraft will want to steer off centerline and off the runway during your take-off roll! Once the tail comes up (tilt angle in an outboard) the steering immediately relaxes and gets better.

When I went on my maiden voyage the trim rod was set in the fourth hole from the transom. Way too high, as it was porpoising badly. I set it on the second hole and it brought the bow down nicely. I will try the third hole and see how that goes. Thanks.

If steering torque is going to be your main objective instead of optimum performance then you can always change the load placement in the boat to match the tilt angle as much as possible. Load farther forward should reduce the porpoising. Load farther aft will reduce plowing.