I think it must just be engine vibration that made the starboard front engine height adjuster nut wind down.
I haven't rotated the engine manually but did crank it using the starter motor before I removed the drive, so chances are that the coupler had rotated to a different position compared to when I fitted the drive.
I've just posted this (below) as a comment on one of Michael Romer's YouTube engine alignment videos, would appreciate your and other iboats forum users thoughts on this too...
I rebuilt and refitted my engine a couple of years ago (1995 Ford 5.0 OMC Cobra / SX collaboration), obviously I removed and reftted the drive at that time. I recently fitted a new gimble bearing, alignment checked OK using the alignment tool and checking spline grease witness marks but it was difficult to refit the drive. I intended on testing the boat with the new gimble bearing one time before winterising but decided just to winterise instead. Working on the engine during winterisation I noticed the starboard side front engine mount had wound down so the engine was sitting low starboard front.. which begged the question why did alignment check OK and how did I manage to refit the drive. I wound the engine height adjuster nut back up but decided to remove the drive and check alignment again, it still checked OK despite having just raised the front starboard side of the engine over an inch. Then as a test I partially inserted the alignment tool and used it to adjust the bevel angle of the gimble bearing, as expected the alignment tool wouldn't fit into the coupler. So I adjusted the bevel angle of the gimble bearing again and now it slots into the coupler again no problem. Seems to make a bit of a mockery of the alignment process? But I have noticed that when the alignment tool is all the way in it seems like the angle of the alignment tool through the gimble HOUSING (metal hole that the gimble bearing goes in) points down at the rear. If the shaft points down towards the rear won't it mean that the shaft will be too low at the rear for the U joints to be in line? It seems I could adjust the engine front mounts to various positions, then by adjusting the bevel angle of the gimble bearing the alignment tool would fit OK with minimal resistance... But do we also need to be concerned about the angle of the shaft through the gimble housing? Should the alignment tool be parallel with the walls of the gimble housing? I am thinking that if it isnt parallel then the drive input shaft rear of the U joints will never be inline with the shaft forward of the U joints... Is that correct and if so would it be a problem? Since my alignment tool seems to point slightly down at the rear when it is inserted through the gimble bearing and into the coupler, should I lower the engine at the front (and partly insert the alignment tool to adjust the bevel / gimble angle) so that the alignment tool fits easily through the gimble bearing and into the coupler when at the same time the alignment tool is parallel with the walls of the gimble housing? It occurs to me that the big difference between the alignment tool and the drive input shaft (other than the alignment tool not having splines or U joints) is that the alignment tool only has to align with 2 components (the gimble bearing and the coupler) while the actual input shaft has to go through the gimble bearing, into the coupler and is also has to be at a fixed position at the rear so that's 3 points versus 2 points. It's a lot easier to get 2 points aligned than 3. How much do we need to be concerned about that 3rd / rear point also being aligned?