After putting it back together does the battery charge? I have seen honda's in the past that had good alternators but had connection problems with the round plug at the alternator. If the battery and alternator passed but it still does not charge I would check your fuses, The main charge wire from the alternator to the battery, and the round multi plug at the alternator. Do you have a repair manual for your car? if not I can look up the wiring diagrams for you.