motor, shaft and boat alignment

IMHO, a slight pull to one side when letting go of the steering wheel is desirable. This helps in keeping the boat going straight ahead when running the course or otherwise. If the steering is neutral, then small waves and such will make the boat "hunt" from side to side.

Now, some boats have anti kick-back helms (not necessarily CC's) that will prevent the steering from self centering after turns. This type of helm does not mean you have a bad steering cable. But, on normal helms, the boat should self center from turns, if it doesn't, you may have a corroded/dry cable or dry (tilt) helm.

your worring about something you cannot change. The shaft alignment will have no effect on the rudder what so ever so suggesting aligning this and doing that is just pissing in the wind.

The reason it pulls now is becuase the rudder is different than it was before. So as the water passed over the rudder it is going faster on one side than it is the other creating a pressure difference and your pull. If you want to try and fix it or make it not as noticeable then you need to file on the edge of the rudder and quite dicking around with the alignment. Personally there's nothing wrong with it. If you let go of the wheel and it doesn't go one way or the other then you need to replace the steering cable or at least lube it, because that is what is keeping it going straight.

If you can let go of the wheel and it still goes straight then do a couple of high speed power turns and it that will fix the problem when the cable breaks. Beacuse it's old, stiff and rusted and need's replaced and a power turn is just the ticket to prove it to you, justy have a cell phone and a tow boat handy to retrieve your boat.

You need to loosen the coupler a little bit and take a feeler gauge and check the gap between the 4 bolts to see if it is consistant. Most likely the transmission has moved over to one side.

It is the nature of the beast to pull one way at certian RPM's. Go faster and it will pull in the other direction.

Your strut determines the shaft alignment. Is there any room for adjustment in the mounting of the strut?...if not, the rest of the alignment is fixed to the strut alignment. Have you changed props? Could the tendency to run to port be due to prop thrust? Is the steering wheel centered? Have you disconnected or removed the rudder cable lately?