Try this if you haven't. Remove the cover from the power distribution box, loosen the battery cable and listen for a click. If you don't hear one, touch each relay one at a time and give it the braille test. But with it being intermittant, you may be better off doing it the hard way.
Use a circuit diagram (schematic) and get some bulb holders. Find the ciruits that are B+ with the key off (other than the keep alive memory circuits), and splice in the bub holders. Let's use the power seat for an example. Logic states that if the ciruit isn't compete (good switch), the light should be out. If the circuit is compete (bad switch or intermittant short between the motor and the switch) and you find a bulb lit, chase that circuit. Yes it's a lot of work, but if I were in your shoes, it's what I'd do.
Also go back in time and examine anything that you repaired just prior to replacing the battery and alternator.