@tungee the colors are set through tcl variables in a .tcl plugin loaded by pd when it starts. An example file with documentation is in doc/7.stuff/colors-plugin.txt. If you change the extension to .tcl and save it in your pd path you will get an example theme I was using awhile ago. From there you can change the hex values or tcl color names to get the values you want.
or you could try @60hz's .tcl file as a starting point (just download the .tcl file and put in your path)
Maybe I should try to mention this on release pages...