I would add the texture to the shader itself, so that it can be applied with code - then take that texture, and add the output to the refracted output, and normalize.
I'm sure it's possible to do it that way, like have a translucent stained glass texture that is included with the shader output. I'm sure some shader guru will come along and make it really easy, but it might be worth having a go yourself, no harm in messing with copies of your shaders, maybe check a texture blend shader like GG's to see if the texturing can apply to the refraction shader as well. It has to get that normal texture reading, so perhaps the shader could get the colour image data as well.
If you can figure that out though, then you'll be able to apply the colouring any way you like - either mixing with the refraction colour of each pixel, or use it as a base colour and use the refraction data to shade it. It may be possible to factor in that Z component in the normal map (height) and use that to change the strength of the transparency - thinner and thicker stained glass would look great.