jjns,
I have a PYI seal that I installed a few years back and don't understand your comment about not being able to adjust the shaft alignment without sinking.
To install the PSS, the shaft needs to be installed in the flange, the flange bolted together, then the PSS bellows can be compressed with the ring to the proper measurement (3/4 of an inch if I remember right), then set screwed in position. Once the boat in back in the water then the flange can be unbolted and the shaft alignment adjusted. The seal works by the bellows applying pressure between the Carbon ring that is attached the the bellows and the SS ring, Additional compression on the bellows will not cause a leak, the bellows will actually alow some misalignment of the the shaft to the stern tube, without leaking. The question is do you have enough room with the PSS installed to open the flange to adjust the shaft alignment and install a safty collar.
I also intalled a split 316 SS shaft collar to aid in the installation and added security. With my shaft all installed and the bellows attached to the stern tube. I pressed the SS ring of the PSS to the carbon ring with out compressing the bellows and installed a split collar behind it just flush. Then I used a couple of pieces of wood between the split collar and the SS ring 180 degrees apart, to hold in the proper bellow compression untill I had the Set screws tight. Then I loosened the Split ring and moved it flush to the SS ring and retightened incase the Set screws ever failed.
McMaster-Carr
I used Part number 9633T19 for a 1" shaft.
I also at the time replaced the existing bolts with ones also predrilled so that I could wire them, also available at McMaster Carr. I actually use a lot of hardware from them, they certify the materials well enough for the medical instruments, good price, right to my door or work so wife doesn't count it against my boat bucks.
I hope this helps, feel free to PM me if you have any questions.
Pat