I do like Tom at Wild Hare recomends, I stand the plane on its tail (befor mounting the rudder) tape it to your bench so it won't fall over.
Set the engin on the motor box mount the cowl on the plane (you may have to rough cut the the hole for the motor head to stick out) and center the spinner back plate so it lines up with the cow.
Then carefully remove everything so you don't move the engen, then take a sharp pencil and mark around the standoffs. mark the center of each hole and drill.
Thats the way I do it.