BluePhaze / L3mon On Visual Studio, click on the Solution, you can rename the name there. Then click on the Actual Name -> Project Properties and you can also change the name there. With those 2 changes, you should notice that the name was changed from WindowsPhonePlugin to whatever you want.
Please note, you also have to change the WMAppManifest.xml
That should work. Do not replace all the WindowsPhonePlugin, because you will break the code (as you already know).
Hope this helps. This plugin is great! :)