takes patience...lots of patience...
put a small towel under the coupling to catch the stuff you drop. Mark the couplings across the top edge so you can put them back together they way they came apart. Unbolt the flanges from each other, seperate, rotate one flange and measure at 90 degree increments, the idea being that if the alignment is off the clearances will change as it is rotated.. Adjust the motor mounts to get the specified clearances. Bolt it back up & it should be fine. Do this with the boat in the water...the aligment changes when on the hard and it may take a week for the hull to settle down after being splashed. Don't be surprised if you have to do the aligment a few times to get it right. Go slow & be patient.