[HardcoreZ28]

Paint the whole thing if you're this far along already. Scuff the entire engine bay and use a primer sealer. Self etch is only for bare metal and you're not going to need to go that far down. I like Dupont Chroma System paints myself. Get a line dryer as suggested earlier and believe it or not the two gun sets that Costco and the like sell are pretty good. One if for primer and the other for color and clear.
As for Tim's statement about them not clearing the engine bays....I could be wrong but I'm pretty sure they always clear them. The cars are painted while they are completely bare by robots and I'm certain that they would be programmed to shoot the whole car with clear if they shoot the whole thing with color. Plus if two stage paint isn't cleared it would be destroyed in a matter of weeks. The underhood paint is just never buffed out so it looks less shiny.
And a very important tip....get a good mask to protect you while you paint and no matter how hot it is wear long pants and long sleeves atleast while you're clearing. If that stuff gets on your skin it will make you sick believe it or not.