Well, the unibstaller jar is created as the last step of the installation. Any other files created by your app must be cleaned up via an unubstaller listener.
I think you can overcome your uninstaller as admin requirements by writing the appropiate registry keys for the uninstaller to start from Add/Remove Programs or whatever is called now-a-day in win8.
You dont need exe wrappers in the ubibstaller, simply call cmd.exe in your own process and delete the folders you want or handel it in Java.
You could start another process via cmd.exe and escalate its right to admin. It shoukd promt the user to acept the right elavation.
I do belive that run with elavated privaledges should work for the ub j bstaller, i dont recall top of my head.