Jim:
FWIW, I spent HOURS (literally!) getting the new engine mounts adjusted so the shaft is aligned properly. Not familiar with your Hunter 36, but from conversing with my mates at our marina, shaft alignment is extremely critical-especially if you have intermediate bearing support or an external strut. Our Morgan 28 is relatively simple in that she only has a 40" prop shaft and no intermediate bearing supports other than the cutlass bearing, but still we found a huge difference in alignment with only 1/2 turn on the mount nuts.
We'll be splashing the Merry Bee in a week or so and I plan on rechecking the shaft alignment at that time.