True. And of course we don't know just what kind of a "road" bike this "hybrid" is turning into. It will never be a racing bike, because there are some fundamental frame geometry issues that cannot be changed. Turning a hybrid into a "road friendly" bike can be as simple as a slight lowering of the handlebars, swapping the knobbies for semi-slicks or invert treads, and slapping a different handlebar on.

However, I still believe the neck pain is being caused by the fact that as the OPs handlebars get lower, he hasn't changed the width yet, or maybe bought a bar in an inappropriate width. The bars are too wide, and that's the root of the problem.

Oh, and to the OP, I don't even know if it's possible on a hybrid convert, but don't put those handlebars lower than the saddle. The geometry should not be right for that anyway.