Hi Josh, I hesitate to offer an opinion on your situation as I haven't done that and I'm no expert. However, your reasoning seems sound and here are a few thoughts.
I'm in favor of shortening the shaft log by cutting. Not sure how much. The shaft log does not support the shaft, it only supports the seal to keep out water, so shortening will not weaken the log. Shortening the log will reduce some of the offset angle if the log isn't truely in line with the shaft. Shortening the log will also reduce the amount of leverage the seal might impose on the log if things are misaligned. I think the seal rubber tube, needs two clamps, but I also think they need to be spaced apart. I wonder if the seal manufacturer recommends mimimum dimensions for that? Without that, I'd suggest leaving twice the minimum distance for two straps. This diagram of a Catalina installation shows 1 1/2" minimum between stuffing box and coupling. That's all you have. https://www.usedboatequipment.com/stuffing-box-maintenance/ Chuck Scheaffer Resolute 1989 C&C 34R Pasadena Md
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