Once things are disconnected, maybe it would be possible to find the correct center by pushing the shaft up til it stops, then down, then side to side. Estimate the center, then get creative with a solution to block it in the center position. This should get you to a happy starting place to move the engine to and use your feeler gauges there. You could double check the positioning again with any blocking removed, but that shouldn't change things.
From there, if there is misalignment through the cutlass, you have more problems. The only way to check that (provided the shaft isn't bent) would be on the hard with a laser through the center of the cutlass pointing to the engine with the shaft removed. It's possible some of that could be taken out by going slightly off center through the log with the shaft, but you really don't know which way to go without being able to see and feel how the shaft goes through the cutlass since the boat is in the water.
From there, if there is misalignment through the cutlass, you have more problems. The only way to check that (provided the shaft isn't bent) would be on the hard with a laser through the center of the cutlass pointing to the engine with the shaft removed. It's possible some of that could be taken out by going slightly off center through the log with the shaft, but you really don't know which way to go without being able to see and feel how the shaft goes through the cutlass since the boat is in the water.
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