I just put a 4*40 ARF together last week. I had the same problem you did. I couldn't figure out a way to mount the battery back there. I ended up just wrapping my reciever in foam and packing it under the front of the servo tray. Then I wrapped the battery in foam and placed it in front of the reciever. (between the fuel tank and the servo tray) I then took a piece of 1/4" balsa and made a brace to hold it in place. It was a litte nose heavy. With 3/4 oz. under the horizontal stab it balances just towards the front of the main spar.
Another thing I did per my instructor was ignore the aileron placement template. He had me align them with the bottom of the fuse. Took 2 clicks of elevator, and 2 clicks of aileron to get her to flight straight and level on her madien.