You fixed your problem and used a 2D array, which is more logical, but I think your blending problem is because, well, in a 3D texture, you also get bilinear (trilinear, actually) filtering, which means if you were just stacking textures one on top of the other, you might end up interpolating two different textures.

I think the problem is you tried to sample the 3D texture "between" two adjacent textures instead of on exactly one, probably by using the z-coordinate = (texture I want) / (number of textures total) trick. This will work, but only if you add a 0.5 offset to your texture number, because of the way sampling works, so you need to use (texture I want + 0.5) / (number of textures total) to sample right on a given texture in your 3D texture (a "slice" of your 3D texture).

The 3D texture coordinates work exactly the same as the 2D and 1D coordinates - a floating-point range from 0 inclusive to 1 exclusive, in each dimension. That said, if you have D3D10, you can use the Load() method to bypass sampling and directly access each texel through integer coordinates (but you also lose sampling, which is not what you want anyway).