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Have you checked the alternator out put? I have seen alternators that fail to charge the battery only after the engine has been running for a half hour or so. check the alternator out put.
Also, don't disconnect your battery again while your engine is running. That's not a good way to test an alternator at all. Could actually cause quite a bit of damage to your electrical components. Check the alternator output voltage using an alternator tester which basically is just a few lights. the more lights the better, or use a DVOM and check the actual voltage. Please let me know how that goes.