Jim, i'm replying here 'cause I can include the pixs to illustrate my point. In the above photo, you can see Bandolera's set-up. The black coupler which attaches to the prop shaft is what aligns with the tranny. Here you can see three of the four winglets of the tranny and at this point, they do not align properly - Those 4 winglets have to sit tight on top of the protruding lip of the coupler. I agree that it is easier to shimmy the shaft than to try and move the engine... HAH! That is also the way I approach mine. Yes, because the shaft is so short, I also feel that once you have aligned everything and tightened it down properly, the movement of the engine relative to the shaft is minimal. When introducing the shaft from the outside, I then attach it to the coupler and slowly try to get the four blades of the tranny to hit their mark properly. I slowly attach the bolts without tightening them totally until I can see the four blades evenly against the coupler with no gaps. Since you have a new cutlass bearing, of course it will allow you to shimmy the shaft a tiny bit, all that is necessary to fully align everything. Then I tighten all bolts. Every time I haul out, I change the cutlass bearing, remove the shaft, clean everything down there, re-pack the stuffing box, etc. then I'm good to go for another three years.
With the boat back in the water, I have never yet found I need to re-align anything. I do check it, with the engine running, and can see the whole unit spinning very evenly. I don't want to spook my tranny, but haven't had a problem with it for quite a long time. If the engine was running with a bad alignment the tranny would break - it did, a long time ago- before I was aware of these issues.
Hope this helps.