First off if you want it to look good its all in the prep, I'm sure everyone will tell you that. Spend lots of time getting it sanded, filled and masked off.
As far as body filler goes I would avoid using the "bondo" brand of anything. It is really hard to sand off and clogs up the paper making you go through lots of it. It also shrinks a lot over time and starts to crack which ends up sucking after you've spent all that time painting to only have to do it all over again. I use Evercoat rage gold filler and I love it. Once I get the filler blocked down with 80, 120, 220, 320 I spread a coat of PPG spot filler over the top of that to fill in some of the small imperfections like small bubble holes. Block that out with 320 and hit it with 3 coats of primer and sand it down with 400.
I'd probably sand off all the can stuff wipe it down with wax and grease remover and hit the whole thing with primer and then block that out with 400. It is really easy to see where you have low spots if you use a 10 or 12 inch block.
After you get that part all done wipe it all off again with wax and grease remover and start to spray on the color.
Paint the whole thing at the same time, if you do it in multiple sessions you'll end up with slightly different colors on the car. I paint all my stuff in my garage and don't have any problems with dirt and dust getting into the paint. Make sure you cover anything you don't want to have overspray on because it gets everywhere and make sure you have good ventilation. I have two windows in mine that I open and put those HVAC filters over the screens so it keeps dust out. On the other side I have a swamp cooler that blows out of the garage to get the fumes out.
Gravity feed HVLP guns are the way to go, they use a lot of air so make sure you have a big compressor that puts out quite a bit of CFM, I'd say at least 12-15 at about 90 psi. Also you'll need a pressure regulator since most guns use about 30 psi at the gun and a water separator at the end of the line where you connect your hose in. I have a paper one but I have gotten by with those bowl type deals just fine. Don't use the hose you use with your other air tools because if you oil your tools like you should you'll end up sending oil through with the paint and have it fish eye on you. Get a new hose to use only for painting.
I really like Dupont paint but it's kind of pricy. The PPG deltron is pretty good stuff and even their Omni brand isn't terrible. Get lots of quart size mixing cups, sticks, and filter cones when you get the paint, they are usually free when you buy the paint.
Lastly have something to test spray on so you can get the gun adjusted before hitting the car with the paint. Also run a strip of masking tape around the top of the gun where the cap goes on, they like to leak and drip paint out of there and that's not fun to get on the car.
I've never done a flat color so I can't help much there, sorry.