Generally speaking, the holes are there for the fuel lines to pass through. Fuel /exhaust residue will usually find it`s way past the firewall which is why it`s recommended to coat the wooden surfaces with something fuel-proof. The holes in the bottom may have been added by the previous owner for some other purpose and probably could be filled with wood putty or epoxy.
Also, look up "Radio Control Info" on the web for the proper servo torque application.