I can't help much with your problems. However, the bell in the back box needs the item shown in your hand that doesn't have a coil installed. If you go to the ipdb.org site you will see a picture showing the bell striking coil and apparatus.

http://www.ipdb.org/machine.cgi?gid=1045

The loose wire near the transformer will be more difficult to resolve. You either need to acquire a schematic for the machine or have another owner shoot some detailed "still" shots of the transformer wiring. It could also help if you were to identify the wire color and tracer if the color is still present on the wire.

The problem of the game going to game over with one ball could be the game ball count unit. I am not familiar with this generic of EM but when the ball goes into the outhole the ball count unit should either decrement or increment via a soloenoid. When the unit reaches the last ball that is likely setable via an option plug to either three or five balls it should go to game over. Again, I am not sure about how the balls are counted on your machine but I would first check and rebuild any of the stepper units as they become stuck and sluggish over time because of old oil and grease turning to glue.

For EM problems, you might also join and post your problem on the EM forum:

http://games.groups.yahoo.com/group/empinbalmachines/join?check_sub=1&last=%252Fgroup%252Fempinbalmachines%252Fmessages%252F20823%253Fxm%253D1%2526o%253D1%2526l%253D1

Have you got the schematic for this machine?