when you get fileref:0 you didnt get it, also you dont need to rmdir at all, everything should overwrite. thirdly you dont need to put services.plist back up if your using windows, although you can do this as a percautionary measure but for the most part, its not necessary. This is just me, but i like to cd into the directory then putfile, i havent had any trouble that way, ive been told you can just putfile, but you may want to try to cd in there first. also when you putfile say calculator, type putfile /Applications/Calculator.app/icon.png (put a slash before Applications, or any directory). other than that you look fine.
edit: if this is not your can of beans you could try manzana
here its a click and drag thing, so no miss types. copy manzana into your phonedmg folder and unzip the contents in there, and run in windows. drag and drop your files into the appropriate directory.