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I think the problem comes from the fact that your black lines are not very crisp and sharp. If you look at this magnification you can see all the fuzziness and gray areas. I believe this is what's affecting your ability to make a clean selection for your gradient. You need to clean up these lines before applying the gradient. There are several possible approaches to do that and I've outlined one below.

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• Make a selection of all the black outlines (the Magic Wand tool would work) and copy them to a new layer.
• On that new layer, re-select all the black outlines. Then go to Select>Modify>Smooth. You can experiment with how many pixels to enter for the smoothing, but try starting with two pixels.
• With your smoothed selection still active, go to Edit>Fill>Black. Now invert the selection and press Delete. This should result in much cleaner black lines with little or no grayish values to mess up your selection.
• Now create a new layer immediately below your black lines and fill it with white. Merge the two layer (the black lines and the white) to give you a brand new blank template for you to apply colored gradients.

Here's what I get (at 200% magnification) after following these steps:

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