I second the powder coating. It shouldn't cost too much if you find the right place. I know of a great place here in Denver Colorado but that probably won't help you much. Talk to the place that did the sheet metal. they should have some recommendations for you.
If you insist on painting it your self then use a good rust inhibiting primer first after a through cleaning. I would use lots of acetone. And remember that after it is cleaned you can not touch it with your bare hands without cleaning again. Oils from your skin are enough to cause problems.
CHad
When the going gets weird, the weird turn pro.