It's a tough situation, and there's no "Easy Way" that I know of.

If it were me, what I would do is this:

First, determine from the "manual" how far the thrust plate is from the firwall, or mount the cowl and measure it.

Place the rear of the mounts flat on a table. Place the engine between them at the proper distance (It would be good to have an extra set of hands) and mark the drill holes.

Drill the mounts and install the engine.

Now place the assembly on the firewall in what LOOKS like the proper spot and secure it with one wood screw in one of the top mount holes.

Trial-fit the cowl and see how close you are.

If you are off, remove the screw, replace the engine and secure it with a screw in the opposite top mount hole.

Test-fit the cowl again.

IF it's good, drill the other three mount holes and install the blind nuts or whatever method you're using.