Re: out of alignment?
got it in a little, splines are on top of tool, sounds like it is time to adjust. Why would it be this far out?
I know man, I think things just settle a bit after time - fiberglass, wood flexes. Based on your description of the markings on the alignment tool I would start adjusting your motor mounts up - probably one full turn at a time. You will be jumping in and out of your boat a whole lot. A second person helps.
Before you get started on that I would probably make sure the gimbal bearing is well seated to make sure you are aligning properly. This is a delicate thing you may or may not need to do and you definitely don't want to damage it. Personally and I am certainly no expert, I tapped the outer race
only with an appropriate tool of my chosing at the 12, 6, 3, and 9 o'clock positions in that order. Obviously, they make a special tool for this, but most of us don't have mass amounts of $$ to afford these. A socket having the same diameter as the outer race would be the next best thing. Never hit the inner race. If you're confident it's seated you're good to go.
Start your alignment adjustments and once that thing starts sliding in and out like you know what you're almost done. Make a mark on your crankshaft pulley with some whiteout, pull your sparkplugs, and turn your crankshaft 1/2 turn and recheck it again. You may very well be doing more adjustments, but at this point I would be making 1/4 -1/2 turns on my adjusment nuts. Keep checking the 12, 3, 6, and 9 o'clock positions using your one whiteout mark until that tool slides in and out easily in all positions. Then lock it in place with the nuts on the other side of the mounts and check again. Then, you're done. Good luck.