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Have you tried testing the alternator using a multimeter while the engine is running? It's good to test an alternator this way because you will know the if your alternator is generating enough voltage to charge your battery. Try this http://automotivez.net/bad-alternator-symptoms.html they have a video of how to test the alternator. Also, check your wiring. Some of it might have been damaged and causing a bad ground to your electrical system.