I've been thinking about this the wrong way. I thought you meant something was drawing too much current while running, but you're describing something that causes a dead battery once in a while, for no apparent reason. Right?I'd like to build a voltage drop data logger to help find what circuit is draining a cars battery intermittently.
In that case I think I'd look at it more globally and have a sort of alarm that triggers when the current draw while "off" is (maybe 2? times) more than whatever the typical value is. This wouldn't identify the circuit but if you could examine the vehicle when the fault is occurring then the culprit wouldn't be too hard to pin down.
Or were you thinking of something that could travel along with the car and log over time, and thereby catch the culprit in the act, in or out of the shop?