A good way to ink something is to use real ink
try taking your penciled drawing and taping a piece of graphix 360 over it. using either copic or micron archival pens for a nice and thin line.
from here black india ink and a #2 sable (or synthetic) brush works well for the thick and thin lines. after a few practice runs with that i would then take your drawing, place it on a light table and get a nice piece of bristol, place it over your drawing and ink that.
scan that in and start to color.
the nice part about the photoshop is you can change the color of the line you have from black to any other color using the saturation tool. I personally like changing it to a nice brown.
you have the right idea for the multiply layer for the initial coloring but after that creat another lay on top of the piece and paint opaquely. since your clines arent black they now become part of the piece and you can eye dropper the color you want. use a little burn adn dodge tool to make the highlights and shadows pop nicely and youre done.
hope this was helpful