After speaking with Sonex Tech Support today and reading the new, detailed instructions they have for installing the rocker arm assemblies, I decided to see how mine would align.
For the most part, everything is OK. One rocker on each shaft appears to be right on the borderline of being on the valve stem (not described well) as per plans, but it may be OK. The bigger issue is that the valve covers don't fit. The valve lash adjuster shafts protrude out just a bit too much which keep the covers from seating to the head.