Electrical issues

I must have left the doors unlocked last Halloween, because some gremlins definitely got in!

It has developed several electrical intermittent problems. I am hoping someone will have had experience with these issues, and know where I need to start looking for the problem. It is California compliant.

1. Security message in the information window comes on and off, but nothing happens.
2. Headlights will start to blink on and off, and the interior lights will do the same at the same time. Opening the driver door will cause the lights to stay on, but stop blinking.
3. Window controls at the individual doors will mostly not work, but some days they work for a little while. Driver master controls work all the time.
4. Driver doors lock/unlock switch mostly works, but sometimes doesn’t. Usually turning the ignition off then back on later will get them working again.
5. Sometimes something will drain the battery down over night. I can start it with a jump-starter battery pack, but then it will not stay running without keeping the engine revved up some. Eventually, (20 min./ 10-15 mi.) I can take my foot off the gas, and it will stay running.
6. Battery cables have new terminals, VOM shows 13-14 volts at battery when engine is running, so the alternator is working, and the cells have been checked with a hydrometer style battery checker.
In May of 2013 I had to replace the engine ECM unit. It was hard to find a rebuilt one with the right part number due to the engine size and it being California compliant. The part number is P56040331AB. The VIN number is 1B4HS48Z02F219887.

Here is a story about the ECM. When I put it in, It didn’t work correctly. The engine would start, run for about two seconds, then turn itself off. Went through heck trying to find out why, and eventually I found out it was because the tire size on the vehicle didn’t match what was programmed into the module. The person who originally bought it had non-standard, over sized tires put on it. I took it to a dealer to re-program it. They got some sort of “differential out of sync” code, and the tech thought the ECU had come from a car with a different differential and wanted to replace the module. I had to almost fight with him to get him to reprogram the tire size, and when he finally did, it worked just fine.

The reason for the story is why I don't want to take it to a dealer to look at my "gremlins" problem. I am afraid they will replace everything electrical before they find the bad fuse link.

Thanks in advance for any help anyone can give!