I took my shaft out last year to check it for staightness. Removing the cutlass bearing allows the shaft to pass to the side of the rudder/fairing. There is a special tool to remove and replace the bearing with the shaft in place. My yard wanted a fortune to do the work and needed 2 weeks lead time (the boat was aleady on the hard). I opted to spend $400 on the tool (
http://www.strutpro.com/ ) to remove the bearing.
I would recommend you remove the coupler at the back of the engine and have the yard R&R the cutlass bearing and prop. To remove the coupler take out the four bolts that connect the coupler halves. Push the prop shaft aft and place a spacer between the prop shaft in the aft part of the coupler and the transmission output shaft on the front half of the coupler shoving the coupler halves back together with the spacer being long enough to prevent the coupler halves from touching one another. Now install the four bolts like you are going to reassemble the coupler and tighten them down until the coupler faces meet each other. This will start to push the shaft out of the rear coupler. Disassemble everything again and install a longer spacer and repeat the process until the shaft is free of the coupler. You will need longer bolts than stock for this procedure. The spacers can be pieces of bar stock, sockets, anything that is smaller diameter than the prop shaft (1"). You may have to use heat and penatrating oil. You may have to cut the end of the shaft off. Then at least you would know the new shaft was straight.
Replace the coupler with a split coupler like this,
http://www.propshopinc.com/4-BS-Split-S ... r-p12.html . Have the coupler machined to be true to the shaft and a slip fit on the shaft by taking both to the the machine shop together.
I would try and stay away from pulling the strut. Replacing it is not all that fun.
Hope this helps.
Jim
PS. Don't forget to remove the set screw from the coupler before trying to remove it from the shaft.