When trying to isolate a current drain, how do I
1) Determine which fuses have current across them with ignition off
2) Measure current drain as I pull above fuses individually

92 500SEL

Takes at least a full day to discharge so its a small drain..

Driving me nuts...a short trip

To check the "rest current" you simply need to connect an ammeter in series between the negative battery terminal and ground. When you have an accurate measurement you simply start removing and replacing the fuses one at a time while keeping an eye on the meter for changes. You didn't say what kiind of car you're working on or what the problem is. On newer cars certain procedures apply. You run the risk of damaging your meter if you're not careful. A little more information would be helpful. Regardless of the vehicle, make sure the key is off/out.

It is usually at least a full day...sometimes two...so it is a small drain I guess...but enough to stop me cold

I've seen alternators cause excessive rest current draw, but it usually kills the battery within a few hours. You can try dis-connecting the alternator overnight and see what happens the next day. If you decide to try this BE CAREFUL!!! Make absolutely certain the wires at the alternator DON'T TOUCH ANYTHING!!! If this isn't the problem you'll have to go back to my previous post. Since your battery is in the trunk you'll need to do a few things. First open the trunk and manually operate the latch with a screwdriver. This will operate the closing assist. Make sure you do this before connecting your meter! I would also suggest opening all the windows. If you need to get into the car while the meter is connected, don't open any doors. When you close a door the closing assist will again activate, possibly damaging your meter. In the past, I've also found that a thorough function check of all consumers/accessories can be helpful. You may discover something not working properly. This may provide some direction as to where you start looking. Current draw problems can be tricky, even for experienced techs, so take your time.

Hi wmkoles
Although ILUVMILS has described it already, let me tell you how my neighbor and I found a small draw on a 78 Honda.
With everything off (no key in) we disconnected the ground wire to the negative pole and messured with the multimeter the voltage between the negative pole and the ground (some shiny metal on car). It registered about .36 volts (The car would go dead if not driven every day). While I watched the meter, my neighbor pulled first fuse. No change in multimeter reading. Fuse back in, next out. At fuse nr. 5 voltage dropped to .018 volts if I remember right. Thus circuit 5 was somewhere draining. Turned out to be the circuit that turns the head lights out when light switched on. One of the motors had earlier quick working and they had manually set the lamps to be out all the time. But that motor kept on draining...
Hope that helps in your search.
Reinhard Kreutzer