Ha, checking alignment at the coupler with a broken shaft wont tell you much!
I would suspect misalignment as the root cause of the failure as well. By side loading the tranny and drivetrain, it will actually dampen any vibration, not create it.
Definitely realign everything upon reinstallation. Alignment starts at the strut and moves forward. If you dont grasp the concept, then either read until you do or take it someone else who does. The aforementioned "mechanic" who thinks they can align properly with the coupler bolts still attached would be an unqualified individual, IMHO.
In regards to shaft length, I cant speak to the proper length shaft for your boat... but I can tell you that ARE (maker of the dual taper that SkiDIM sells) measures shafts a little differently than what you commonly see (end to end). I would get a measurement from the end of the strut to the transmission coupling and add 1/2". Tell them thats the length of the shaft you need from the front of the prop hub forward- that should be enough information for them to determine where to put the taper.