To align the shaft, you need a good set of feeler gauges. With the standing rigging adjusted, and boat in the water for 24-48 hours, first verify that everything is true. (That is, the faces of the couplings rotate without wobble -- you can measure the gap, then turn the half-coupling a quarter turn in relation to the other face, measure again, and repeat. Ideally there will be no variation. If there is variation, this will greatly complicate the alignment process.) Raise or lower the proper corner of the engine until the center of the crankshaft coincides with the center of the drive shaft. You may have to raise or lower all four points at first -- it helps if you are a contortionist and have good mechanical aptitude, but it is not all that difficult. When the gap at the coupling is the same at 6 o'clock, 12' o'clock, 3 o'clock and 9 o'clock, you are done. Tighten the engine mount nuts to proper torque, then re-check the alignment AFTER the bolts are all torqued down. It is likely that you will find that you cannot get the faces perfectly aligned. After playing with it awhile, you will deduce when you have it as close as possible. It has been said that you should have no more deviation than one thousandth per inch of coupling diameter, in which event, you should be okay with .003" deviation.