Open up the GOTR batch file, and press X to clear all optional mods. Press 1 to go to Controls and Onscreen Prompts, then press 1 to enable the Xbox 360 onscreen prompts. Return to the main menu, and press P to build the custom patch for GOTR with only the onscreen prompts. The files should be in the MY_CUSTOM_PATCH folder. Drag those into the Saints Row 2 folder. Now drag those files into the Saints Row 2 folder to replace the ones in there.
Whoops! I'm stupidNo, it doesn't work that way. The base build of GotR contains tons of base mods, even if nothing else is selected.