Intake manifold painting

If you are determined to do it without removing it, all you can really do is try to clean it as much as possible, prep the surface properly, mask off anything you don't remove from the manifold, and have at it with a spray can of the new color. Not all clear coats take paint well. At the very least, you are going to want to degrease it with alcohol or something stronger, scuff the surface with a grey scotch-brite pad or finer grade sandpaper, wipe it down with solvent again, and hit it with some compressed air and/or a tack rag before you spray it.

But personally, I would probably just put up with the yellowed clear coat until you are ready to pull the manifold, have it shot blasted, and paint or powdercoat it properly.