All done now. Well, the holes are drilled, anyway. I'll have to remove the motor again to install the canisters, throttle and probably a few other things, but the hard part is done.
I stood the plane up on its tail, set the motor on the new motor dome, leveled the cylinders with the fuselage, then installed the cowl. I used a piece of string, measuring from the propshaft to the cowl. When the measurements were equal all around the cowl, I removed the cowl, marked the engine location on the firewall, removed the engine and drilled out the mounting holes.
All in all, pretty simple, and it turned out looking better than I expected. I need to paint the black plastic again to cover up some of the leftover glue and fiberglass from the old motor dome extension.