the shipyard guy says either the prop is on wrong or the tranny went out just as I pulled in to get hauled out for the new stut.
$0.02 from the designer of many marine powertrains:
Some important points haven't come out here yet. Which shipyard guy said that? If it is just a worker bee, blow it off. If it's the guy who will be making the decisions about what to do next, you have a big problem because he knows &^%#@(*& that he's spouting crap and they are trying to avoid redoing a job they know they screwed up. If they can BS you for a couple more weeks Alaska sailing season will be over and they can work on it all winter. Hold off even mentioning lawyers until the last possible moment but I'll bet you are going to be talking to one before this is over.
Cheerfully ask them to verify. Disconnect the shaft and run the engine. It should easily and normally run up to mid RPM in forward and reverse. You should be able to easily turn the coupling by hand in neutral. The prop can only go on one way so, unless you put on a different one....
Is there a bearing just behind the stuffing box or any other bearing in the shaftline aside from the one in the strut? Usually there isn't on boats like this and the stuffing box has a hose. (BTW, if there is a hose, replace it now regardless of how good it looks.) Single bearing shaft lines are very tolerant. Alignment will be more critical on a two bearing system.
If it is a two bearing system, you should be able to now just try turning the shaft. It should be easy to turn by hand. If the boat is out of the water, you have to be sure the Cutlass bearings are wet with a hose which may be difficult with some shaftlines. If it doesn't, the strut needs to be ripped out and reinstalled. I'm assuming that strut was glassed into place. If it is bolted on, it can be shimmed or the glass under it ground down to get the proper alignment. The shipyard needs to consider the scale factor if they are working to the tolerances they are used to on large fishing boats. Do they ever work with small shaft lines like this?
If there is a single bearing in the strut and a flexible stuffing box, you should wedge and block the shaft coupling exactly in place before disconnecting the engine. With either kind of shaftline, any visible shifting of the engine or angular misalignment of the coupling halves after the bolts are removed immediately indicates the source of the problem.
With the single bearing / flexible stuffing box arrangement, remove the hose (which you should replace anyway at every opportunity) and block the shaft exactly in the center of the forward end of the shaft log. Now put a feeler gauge at the top, bottom, and each side of the stern bearing forward and aft. There should be no clearance at both ends of the bottom and side and top clearances should be the same at each end. Lubricate the blocking so you can verify that the shaft turns easily.
If all this checks out, you may have bent the shaft when the old strut failed.
There is a lot more to this. I could go on for pages but I'm out of time. Besides, the shipyard has to be honest and competent regardless of how much advice you get on an Internet forum. I'd be glad to keep giving you what help I can but I'm leaving shortly for a 20 day cruise away from Internet contact (one of the big reasons to go cruising now
If you go to a local Cat dealership, they will probably give or let you copy one of their standard manual sections on shaft alignment. It's directed towards big shafts but the prinicples apply. Othere engine companies have similar publications but Cat's were the best the last I looked. I wish I could go to the office before I leave and could send you a pdf.
Good luck.