I think, this question about customizing the themes should be re-opened, because the master questions are not really asking this question.
Master question 1: How can I configure Unity?
This question deals with configuring various aspects of Unity, such as chaning launcher icon size, animations etc, but It do not with changing theme colors, theme's font color etc.
Master question 2: How to change GTK+ theme?
This question deals with changing gtk themes in newer versions of Ubuntu, where we don't have the option to select other installed themes as was before. It also don't do anything with customizing themes themeselves.
What I understand is, the question was asking changing theme's window colors, selection background colors, selection text colors, input box background color (the background color in search entries etc) , input box text colors etc, which was an option in the older Ubuntu releases (before Ubuntu 11.10).
I saw a question which ask changing selection color but that question wasn't broad in scope to include this and for that, we can't dupe this to that question.
You can execute this command to see the types of customizations asked (If I understand the question correctly):
gsettings set org.gnome.desktop.interface gtk-color-scheme "fg_color:#000000;bg_color:#2f568;fbutton_bg_color:#E5CBCB;backdrop_selected_bg_color:#F0C5B4;base_color: #F0C5B4"
