I'm with mischief. Anywhere you have rust you need to get that taken care of. By a pro. The paint needs to be removed to expose the bare metal and then it needs to have some kind of media blasting to remove as much rust as possible. If the metal has rusted through completely you will either need new body panels, or get with somebody that could do good enough work with sheet metal to fix it without using a lot of bond-o. Meaning cut out the bad section, and weld in new sheet metal in the right place. Quick easy fixes, bond-o, will look like crap in a few years as it starts to crack and pull away from the metal.
I really don't care for partial paint jobs. So if you get a good amount of body work that requires several panels to be repainted, just repaint the entire car. My Ti had some body work done before we bought it, and you can now very easily tell the difference between the stock paint, and the door that was repainted along with the panels where the painted was blended. BMW does an awesome paint job at the factory, and anything that is repainted using lower quality paint will show up in the future.
The loose panels are easily fixed with new clips as mischief already stated. For the cracks in the front bumper, a replacement bumper is the only way to fix that. You could bond-o it, but as the bumper starts to split more, it will look like crap and no telling how well it would stick to the plastic. You may even be able to find some kind of plastic sealer to fill in and rebond those cracks in the bumper. May require a repaint.
You could get the muffler media blaster and then paint it with high-temp rusted proof paint. Probably cheaper to buy an aftermarket muffler.
Photo Day with the Ti 
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