Pull the mid-shaft bearing carrier and make sure the pump is aligned - the prop shaft should be centered in the hole with the pump bolted up. (You may be surprised how many shims under the pump ears you may need).
Then slide the bearing carrier/mid shaft assy on and it now should line up with the locating dowel, 3 bolt holes and be near flush and square with the bulkhead as possible (they also have shims for that too). The goal is to seat the bearing housing with the bulkhead with minimum deflection force put on the floating bearing housing when it's time to torque everything up.
THEN align your motor/couplers without the do-nut - I think the tolerance is like 1 or 2 mm but have seen many get away with much more.
The first 2 alignments are more critical to shaft life than the coupler alignment in my experience. Stricky, and Jason went thru 3 shaft sets before we figured out the problem.