effect of changed thrust line.

How does a person determine what the proper height of an engine should
be when building an airplane? If a particular engine design mandates
the prop is 4 inches, say, lower than where it would be with the
engine originally installed, what effect will it have on handling, and
what changes in downthrust might be advised?

We are building a Pegazair, and my Corvair engine would need to have
the cowl higher than ideal to keep the crank centerline at the same
hight as say, an O200. Weight wize, the engines are just about
identical as equipped Have not determined the center of gravity of the
engine yet, to determine the overall length of the mount.

For those unfamiliar with the plane it is a highwing STOL 2 placer
roughly the same size as a Cessna 150 (150 sq ft wing,33 ft wingspan,
)