I have a fairly similar setup to Morningbird.
Gearbox flange -> coupling -> stuffingbox (with 7inch tube) -> stern bearing (loose fit) -> strut with cutlass bearing -> prop
My 3-cyl diesel is on 4 rubber mounts (new).
At the coupling, I am installing a new Vetus Bullflex coupling plate, which has rubber parts and claims to allow a 2 degree misalignment.
I am attempting to do my shaft alignment on the water today (Friday 6 Dec).
When I played with it a few weeks ago, I got the impression that I will never be confident of getting a 0.003" alignment between
the gear flange and a simple steel flange on the shaft. That's why I got the BullFlex.
Now I know that you want to minimize any misalignment as far as humanly possible, even if you use the BullFlex. So I'm still trying to align.
My 1-inch prop shaft at the gearbox flange is drooping a bit, so I'm not sure how to counter that. If you just pull it up with a strap, how can you be sure that you're not pulling it up too far, making a reverse droop? I've heard Nigel Calder suggests you calculate the weight of the free end of the shaft and pull it up with a scale to match the exact weight. Sounds very fiddly. Will have to see whether I can work out some alternative approach.