colors are defined in the theme's gtkrc file. (/usr/share/themes/lcars-padd/gtk-2.0/gtkrc) Or if you don't feel like digging through that to find what you're looking to change, you could also edit the colors in the theme source image, and rebuild the package.
I'll try to submit bug reports to the maintainers of those apps you mentioned, but I'm kind of busy right now and I can't promise I'll get to it right away.