things that need to be changed to customize the MonoX look and feel are:
/App_Themes/Default/*.css (and images)
/App_Templates/Default/*.* (Change only the templates for WebParts that you will present to a client)
/MonoX/ModuleGallery/ - ONLY mark-up files for WebParts that you will present to a client - NOTE: You need to change mark-up files only if you want to change the layout of the WebPart
You will probably need to do that in short period of time so I'll suggest you try and use something like this
Let us know if you need anything else.