3.42 mA isn't enough to kill a battery. If you were seeing ~1000mA, maybe.
I agree with you about the alternator, might be cooking the batteries.
FYI, there is a wire that bypasses the fuse box. It's the one with the infamous fusible link. It splits off the battery in the trunk then goes to the passenger side positive terminal block to power all sorts of stuff like the DME, fuel injectors, etc. But I don't think that's your trouble.