04 Sierra Crew Cab 1500 5.3

[Valco1318]

Hello,,
My truck is factory stock other than radio, which has been in it for 5 yrs. 135,000--always serviced (by me) and I also do things to it, so I dont *have* to do things to it (I keep it up nicely). Never crashed, abused or stolen.
New batt about a yr ago. Got in it the other morning and dead--and I mean dead-dead.. Disconnected/removed battery and put it on chgr for several hours. Load tested battery and its good. When I go to hook up neg battery cable, it sparks. It always sparks a little, I understand that but this is *more* of a spark than usual. I'm thinking voltage/current draw. I did everything to trace it down but cant find it. 
1. Unplugged and took the cluster completely out
2. Disconnected the alt
3. Took the flasher out
4. Pulled every fuse out of the indoor panel---all fuses were out, laying on the carpet.
5. Started pulling fuses one by one under hood,,made no difference.

So after futzing with it for awhile, I noticed the automatic pass side mirror will not work using the button on drivers side panel, and neither will the window. The window also wont work with the pass window button.
The driver side mirror and other 3 windows work, and so does the door locks---*sometimes* .
I also noticed,using a test light that the test light will blink rapidly ""with the flasher completely removed"". 
The key fob is about 3 months old and worked perfectly,but now I cant program it and the alarm goes off when I try to program it . I did everything short of replacing the ign switch and the key cyl. 
Like I said, everything was fine until 2 mondays ago---*everything was perfect*. 
All of the lights and other accessories still work--wipers/AC/ brake and headlights
I didnt write anything down as far as what did what during my tests, but everything just started doing weird stuff as I was testing things like a damn ghost or something.
I *really* like this truck, but divorce just got finalized and I went out 2 days ago and bought a  brand new Silverado. 
I was in the trade for a very long time, and I'm in no mood to start throwing parts at it.
I want to take it to Carmax to sell it, but I really think this problem should be fixed first.

Thank you for your time and help,

Troy C Cagle