The texture pack is written to hook into MCPatcher's Connected Texture rendering features! If you are already using MCPatcher, or are interested in using CTM Textures, then make sure to follow up with Kahr's Work! (It's the same resource pack, it works in both standard installations, and MCPatcher)
xXTerra_BrandfordXx - Made a lot of this possible, and created many of the CTM resources. I maintain the project, but Terra's hard work made it possible!
Can I Use this In a Resource Pack/Redistribute?
If you would like to use this in a large resource pack, please send me a message, and I'll be happy to respond. Do not host this work alone on other servers, or submit this as your own.
That... and feel free to deconstruct the resource pack I made. I can't spend too much time debugging the problems you have, but if you have all of the files there, you can try to use my Configs for MCPatcher... (Which you may be doing already?)
Edit: Yes... I had to remove Better Glass, so then I just added CTM textures and configs for clear glass and panes as well... Sorry, I thought you were having a problem running my resource pack. I didn't quite realize you were making one yourself.