An update to this thread: everything is back together and she is going in the water within the next few days (there is a boat blocking me waiting for her wheels to be put back on, so nothing happens until they launch her; she is too big for the lift to get around)
The props were checked electronically and found to be fine. The shafts did require straightening, but I don't know how far out they were- unbelievably, they would not tell me. That is something I would have liked to know. Next time the shafts need worked on, they will go to another shop.
The cutlass bearings are all new- the yard installed them. The ones in the struts are held in with setscrews; the ones in the stern tubes have a combination of adhesive and setscrews.
We realigned the engines after everything was back together, before tightening up the coupling bolts. I will run the boat for a while and then check the alignment again. Interestingly, starboard engine needed to come up about 3mm, which seems like a lot. Port was almost right on the money when it all went back together.
My friend who did this (really I handed in tools and did some of the easy parts) used to have an identical boat to mine. He went through several changes of engines in his 36C, and commented that from on the hard to in the water, the hull shape actually changed very little and generally the boat did not require realignment once it had been floating for a while, but we won't take any chances.
We also fitted a hose clamp to each shaft, next to the rotor. The Jesus clamp, as he termed it.
The PSS kits have changed a bit. The rubber bellows is more robust and springier than the old one, which is interesting since the first ones lasted about twice their designed life. As far as I can determine, everything else in the kit is about the same. The kits come with new o-rings, new setscrews, new hose clamps. It is difficult to compress the bellows to the required 1"- you have to use a small pry bar and put some mojo on it.
The shafts turn fairly easily with one hand. They certainly don't spin, but they didn't before. When sprayed with soapy water, they turn more easily yet. I suspect there is a break-in period to seat the shafts into the new cutlass bearings.
Report to follow once she's launched and I've run her a bit.
I did not add the crossover line. PSS recommends that you do that if the vessel will run better than 12-14 knots on one engine. Well, so far my Cummins engines have been very reliable, but if one quits, I will limp home at idle speed, I think.