Do not run the engine with the alternator disconnected. I destroyed one once, doing just that. With the multimeter connected in series with the negative to earth (do it on the 10 amp setting), there should be a quick spike in parasitic draw, for the clock and sound system, etc, then should drop to bugger all. If it is above the small milliamp range, then try pulling fuses and relays, before disconnecting the alternator.
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