A 1998 Jeep Grand Cherokee has gone through 3 batteries in the last 3 months. While they have all been replaced by warranties, it'd be nice to get the problem solved permanently. I've tested the alternator, and it's not defective. I'm suspecting it might be a short somewhere in the system. How can I track down if this is a short, and if so, where the short is occuring?
Standard digital multimeters can measure current and help you identify what in your vehicle is consuming your battery's juice. Get an electrical diagram of your vehicle and try to narrow it down by doing current measurements in the various major paths of flow. When your car is off, no (or only trace) current should be flowing. Every time the path of electricity splits, you'll have to test each to determine which one is drawing the juice. There's no telling how many of these you'll have to check before you reach the problem.
This answer of course assumes the juice is being drained while the vehicle is off. I suppose it is possible that it is draining while on also. The way to rule that out is to disconnect the battery while the vehicle is running. If the car immediately stops, you have a different problem on your hands. Either the alternator is bad or it isn't able to produce enough juice to keep up with your vehicle's demand (which probably includes some defective component that is sucking lots of juice). If it keeps running normally, it might be worth checking the leads coming to the battery (while still disconnected) with a meter to ensure it is being fed properly by the alternator.
By the way, please do this before doing any more battery exchanges. You are making the price of my next battery go up by taking advantage of the return policy like this.
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In addition to an unexpected electrical load, as covered by Captain Claptrap, there are other things to check.
The two biggest killers of lead/acid batteries are overcharging and vibration. Unless you have the equipment and the skills to use it properly (in which case you probably wouldn't be asking) I suggest you get the charging system checked by an independent auto electrician.
For the vibration issue, check the battery mounting. The battery should be sitting very solidly on a surface without any hint of rocking. Remove any mat this might sit under the battery before checking this. That surface in turn needs to be mounted very solidly, with absolutely no sign of movement relative to the rest of the car. A common problem with some cars is that the mount has supports which attach to the fender, which can flex a lot.
If all the above checks out ensure the battery hold-down does its job properly and does not allow the battery to move at all.
If you find any issues with the mounting, no matter how small, have that fixed under warranty, otherwise you're just going to keep replacing batteries.
Find your fuse box diagram. With everything off, pull fuses out one by one and use a multimeter on the fuse socket to measure the current drawn through that circuit. That will give you some indication as to what is causing the power drain.