Is there any way in mountain lion to change copy paste shortcut keys?
If you want the copy shortcut to be command-C, map the physical alt key to control in Windows using https://stackoverflow.com/questions/229633/how-to-globally-map-altgr-key-to-alt-key#396859.

If you want the copy shortcut to be control-C, change the Control key to be the Command key in OS X in System Preferences -> Keyboard -> Modifier Keys..., and then change the Windows key using the same method as above.