The "lite ply" (not balsa) piece is for the rudder and elevator push rod tubes. It goes in at the back of the servo tray accross the former.

If the engine mount is metal the holes are for screws used in clamping the engine in place. four screws and two metal bars that should line up with holes in the engine mount clamp down on the tabs on the side of the engine. That mount does not bolt down the engine through the holes in the engine mounting tabs.

If you want this is a great time to consider some options.
I have an Avistar that I have modified:
bolt on wing
dual alieron servos
tail dragger

It is nice to have something a little different!