Hey bakuryu
I have almost finished with my car. I had the same problems with the old color showing up. What I did, in between coats, it was to go with the roller and paint those spots one more time. It worked.
When I start painting I got a lot of orange peel. What helped me to improve my painting technique was to avoid to paint when the metal is hot and follow the method described for this guy who paint old cars with a brush in England.
http://www.stephen.hull.btinternet.co.uk/brush.html
It is kinda cheesy but it really worked. I hope this help