Intake manifold painting

If you are absolutely sure you're not willing to take off the intake: Take off everything in the way and then tape/paper/plastic-wrap around the intake. If the clear coat isn't showing signs of delaminating anywhere rough sand it with some 180 grit all over and then 320 to take out any of the big scratches. Clean up the whole surface with some acetone. I would recommend you redo taping and masking so there isn't any clear-coat powder to get blown into your new paint. This time I would go as far as taking off the valve covers and covering them off with cling-wrap so you can spray at a low enough angle... still may be difficult to spray into all the nooks the airgap has. If you remember which brand of clear you used I would try to get the same brand for your color. You will have better chance of not having a bad chemical reaction between them. I would spray a small test spot first and see how it reacts. If it reacts badly you may still have to bite the bullet and remove it for media blasting.