On most boats (I am familiar with) you have to adjust the height of the engine/transmission on the motor
mounts. This changes the angle of the engine/transmission relative to the prop shaft. You don't adjust the prop shaft itself. It is what it is. But this can be a very challenging job, requiring a good mental ability to imagine the geometry of the engine
and the effect of each adjustment to the alignment. And you have to be sure and lock in the adjustment after it is done (and check again).
It can be very tedious with lots of trial and error. But it is doable with patience. Make sure you motor
mounts are in good condition while you are at it and replace if shot.
And the prop shaft mounting plate has to be seated right and tight before you start. It has to be dead nuts perpendicular to the prop shaft itself or it will be worse.
You can rough adjust on the hard but the final adjustment should be done in the water as noted.