To start with the engine;s cavitation plate ( the one just above the prop) should be in line or just above the bottom of the hull.
If you using a Stainless prop you can usually go one hole up.
You will know if its to high because it will cavitate in a straight line if your running light and cavitate lots when your turning.
If the engine is to low it usually tends to make the boat bow steer, you might find the boat will lean the wrong way when turning.
What sort of revs are you getting out of the engine? You should be able to get 5500rpm max from a 90hp, when trimmed out, do you have to trim it along way out to get it to rev up?
If the engine is to low it will effet your speed as there is more drag in the water and you probably wont be able to rev to the max rpm without trimming out so far that the boat becomes unstable.
Hope this helps