The best way to check the height is to get the boat on the plane at normal cruise speed with medium load and look at the anti cavitation plate above the propellor. It should be just visible above the water. If it is buried you need to lift the engine another hole or two. If it is above the water you may need to lower it.
You will need to test again to make sure you don't get excessive ventilation. But as with most things on boats, it's a compromise.
Taking measurements from the line of the bottom of the V is a good starting point but each engine/hull/prop combination is different.
Good luck, let us know how you get on.
Try this link for more info.