I don't have your answers but best bet is to do a voltage drop test on each fuse. Basically you put your volt meter on it's lowest reading and put the probes on each side of the fuse. They should be under a half a milli-volt I thnk. If I recall correctly anything in the half volt range or more is suspect. This is with all the doors closed long enough for everything to be in a sleep mode. You may need to clamp the door switch so it thinks the doors are closed. If this isn't intermittent then you can pull the fuse in the suspect circuit and see if the issue goes away.
As for the alarm, it wouldn't surprise me if it went off as the battery was getting to a low state.
Here's a decent video:
YouTube
Here's a website with info:
Testing Parasitic Draw via Fuse Voltage Drop
BTW, one common drain issue across all vehicles is children putting coins in the radio.
Keep us posted.