To add to your list of things to check: From inside the wheel well, at about where the footrest is located, several sheetmetal pieces meet under that tarrish coating that dries up, cracks and lets the water seep in and rust the sheetmetal and let the water slowly make its way into the vehicle. I had that issue, but mine is an 05. From your pics I do not think that this is your problem, but keep it in mind for the next years.