Re: shaft alignment
After correcting the strut you will have to realign the shaft at the transmission coupling. This involves separating it slightly and rotating it while checking the gap with a feeler gauge. The gap has to be very precise - less than 0.007" runout through a full rotation - your specific engine & trans combo will have a spec for this.
With any luck the runout will be vertical and can be adjusted with the nuts on your engine mounts. If it is horizontal you have to loosen the mounts and pry the engine sideways - this can take many tries as pry-bars are not nearly as "fine" an adjustment as the threads on the mount studs.
The fact that your strut is bent means a fairly high likelihood that you will need some horizontal adjustment.
Do it initially before launch in case something nasty pops up but you will have to do the final realign in the water because the boat will flex somewhat after launch.
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