Check ground connections, clean terminals under the hood, giggle and wiggle.
Sorry, I'm afraid you may have gone past some basics. You may not have, and if so, nevermind!
You need about 20 mins. on highway to charge a battery, and many short trips will kill it...especially in the cold.
Hunting a parasitic draw is a pain. I did it years ago. Turned out to be a bad battery. Even a new battery needs to be driven enough for what you're asking of it. Just saying.
Oops, OP, I skimmed reading just to say this, and then I saw that you 'looked' at terminal connections under hood.
Guys have had luck by removing the connections and looking underneath. Also there are a couple of monster groundstraps in the engine bay...also wherever the battery ground connects to.
Work the initial stuff thoroughly before jumping too far ahead. Alt connections? AM electronic device installed? All suspect.
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Mangofy your E46!
Last edited by dmax; 08-05-2011 at 02:52 PM.