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Is it possible that you hooked up some of the wires on the alternator reversed. An alternator has to be "exited" meaning that you need to put a little power in to it to get alot of power back out of it. If one of the wires you hooked to it was a "constant hot" (on all the time) and not a "keyed hot" (on with the key) the alternator itself can drain the battery. If you are sure this could not be it you're going to need to put a multimeter on the battery and pull and replace one fuse at a time until you find the drain. (It will stop drawing when you pull the right fuse) Be careful because the clock/radio is a constant drain but a very small. Save that fuse for the very last.

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Q: What would drain your battery after replacing alternator and battery?
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