Update. I fixed both issues. I take off the door skin, and was just looking for things it could be. while I was there and could see all them, I sprayed down all four window tracks with silicone grease. Ran the window up and down a few times, and other then the window rattling alot, I couldn't find out what it was.
For the light, I wondered if the metal door stoper could be adjusted. So I loosen the top screw, and take the bottom out all the way, and sure enough, there is a centimeter or 2 to move it. So I put the bottom screw back in, move it all to the left (more into the door), tighten the screws down, and sure enough, my door no longer looked like it was open a crack, and sat flush. For anyone with this problem on any honda, try this. I take it for a test drive, the light never turned on once. Success.
Now for the rattle. While testing out to see if the light would turn on, I pretty much tried to find the roughest streets in my town. So I just started grabbing parts and see if that would quiet it down. I held on to one of the window tracks, and the rattle disappered. I could move the track back and for a little, so when I got home, noticed that the bolt was loose. Grabed a 10mm, tighten it, done, no more rattle. I love when problems are fixed so easily.