For quite some time now I am using Testor model paint. Before I used sharpies and paint markers from Sanford. I found that the Testor paint works very well. It comes also in a wide variety of colors and they have also some flat paints. So far, I have had no problems and I used it for about 50 pens. The paint I apply with a small brush inside the blank and out side the tube. I use two coats each. The paint must dry over night, especially inside the blank it may take quite some time to dry I found. Make sure you drill the blanks a tad wider, if the unpainted tube already fits snug inside the blank, it won't go in after the painting.
Normally, I drill 1/64 larger. To glue the painted tube inside the painted blank I use only 5 min epoxy from Devcon - great stuff. Have heard that someone is mixing the paint also in the glue - have not done this yet.