Look through the checklist at the top of the forum and it should help explain some things.
You have the 3rd gen jetta, a3. You have either the 1z or ahu engine according to your year. If your injection pump has ribs on it it's a ahu, if it's body is smooth it's 1z. Minor body rust where? If it's on the doors you can always replace the doors if it's really bad. A body shop should be able to fix small rust pockets but expect to pay at least $1000, depending on how much you paid for the car, it may not be worth it.
To max mileage, drive with a light foot, do all maintenance. A chip, nozzles, and 5th gear mod will also help, see the faq for more details on those. Making the car lighter will also help.
They sell spray on rust stoppers, it' wont cover the rust, it'll just help seal it. Scrape as much rust away as you can, wash, and spray on the rust stopper. Then cover with touch up paint. If it's just a superficial bubble, it might be better to just leave it there.
Also wash the car, the underside, and inside the fender wells. You'd be surprised how much dirt and crap gets caught under the fender plastic liners.
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