It's a touchy-feely thing,
as in 'feeler gauges'. I suggest a search on this site. But here's the short version. Alignment is dictated by the strut. It aims the shaft at the engine. The shaft is also positioned by the shaftlog. The log isn't suppose to change the direction the shaft points to, but just supports it. If you understand the concept then imagine the coupling on the shaft, pulled away from the transmission. The face of two halves of the coupling have to move together and join with bolts. Think of a space capsule joining another spaceship. Clunk, contact, capture! What you need to do, just before capture, is use a thin feeler gauge between the two halves of the coupling. Shoot for 0° error measuring at four points, 90° from each other. Do not try to move the shaft. It's angle is fixed. You'll notice that it can droop when not connected to the engine. That's OK. Just bring it forward to the engine coupling and try to contact it. Then push them together and measure. Another way to measure is to use pieces of a torn matchbook cover. Insert the pieces at the four 90° locations. Pull each from being captured and try for an even pull. Close is good. Now this all assumes that you understand how to move the engine mounts so as to position the engine to be pointing with the shaft. Think of lining-up a gun sight. All movement is done at the mounts. Try to get it as close as possible before launching. After you splash, wait a few days so the hull settles and do it again. And you get to pretend that you're flying a space ship.And yes, on our boat with the dog's waterbowl on the cockpit floor and motoring at hull speed, the water is flat and calm.