You have to align the shaft to the Cutless bearing and hope that in the process it is also centered in the shaft log or stern tube. If you have it aligned to the bearing and it's not centered in the shaft log, but it's not contacting the edges as it rotates, then go ahead and align your engine to the new shaft position and you'll be fine. If, however, your shaft will contact the edge of the shaft log as it rotates, then I'm afraid you're going to have to shim the strut to put the Cutless bearing and shaft log back in alignment. Whatever you do, don't just push the shaft to where it's centered in the shaft log, and not pay attention to whether it's properly aligned to the Cutless bearing, or else you'll introduce a bend in the shaft, which will give you vibration under power and accelerated Cutless bearing wear. Alignments are slow, tedious, and frustrating jobs. Good luck.
