Kito:
I decided to participate in this thread because I recently had to replace my cutlass bearing ... and we have same vintage (although different models) of Cherubini Hunters. Post #10 of the below thread has a detailed description of my strut replacement.
http://forums.hunter.sailboatowners.com/showthread.php?p=1123679&highlight=cutlass
In my case, when I first fitted my new "exact replacement" strut through the shaft, and then dry pressed it up to the mating surface of my boat's hull, the binding was so severe that shaft wouldn't rotate by hand. So modification for the final fitting was needed as I describe in my linked post. While your V-shaped strut mounting might not be so extremely off as mine initially was, my first impression when reading your accounts is that your most probable cause is that your new strut is not of compatible size for a direct replacement fit, or it has been positioned wrong. The recount of my experience in the linked thread might give you an idea or two to follow-up on.
Not sure about your boat, but I am confused about the shaft log being part of the adjustment process. On my boat, the shaft log is a piece of special-purpose hose which is clamped to the stern tube fitting on the aft end and into which the stuffing box is clamped on the forward end. If the shaft/coupling isn't supported between the stuffing box and the coupling, maybe the shaft will droop down a bit because the log hose does flex, but the log on my boat is not really "adjustable" in respect of the alignment procedure. Primarily your new strut has to be the right height and correct angle in all directions so the shaft goes through the center of the stern tube (hence also through the very center of the log hose and stuffing box), and then the coupling must match up exactly to the engine's transmission plate. The shaft should rotate freely with no binding and the shaft should pass evenly through the cutlass bearing with no obvious pressure on any side.
I would think if you don't achieve this before launching, it's probably too out of whack to expect that another engine alignment after launch will fix.
I would get all perfectly aligned before launching. Then again after launching before you use the engine too much.