A friend of mine helped me cleaned my heat/cool unit. He moved it away from the wall. He took all of the wiring off and made a sketch in order to rewire it the same way. He also mentioned to me that he had seen the thermostat kind of loose so he wiggled it and he saw some loose wires so he then proceeded to open it up and rewired it. When he turned the unit on, the transformer shorted out. I then replaced the transformer but it shorted out again. What can be causing this problem??

The transformer keeps shorting out means that something is wired incorrectly. If you cannot find the problem I suggest you call a professional of a ON SITE inspection.