Re: procedure for aligning engine?
With that set up the rear mounts are preset, and not adjustable, you shouldn't ever have to shim those mounts. Adjust the front shims up and down as needed, when you pull the alignment tool out, you should be able to see the groove marks in the grease on the tool compelelty 360 degrees around it.
If you mind marks on the top, extremely visible, and little or no marks on the bottom, then your mounts are too high (picture the angle of the motor in your head, angling the motor up would make the grooves dig into the tool on the top side, and the grooves would barely tough the bottom side.