I admit that I haven't read all your post, but, to spare you some time, Time Machine and Carbon Copy Cloner will not backup your Windows files/Bootcamp partition, period, no point in making experiments with that, won't work. And even if they could neither know how to write back to NTFS volumes to restore files.
For incremental backups of Windows partitions/bootcamp look for Windows specific solutions, there's no unique universal solution that can make incremental backups of osx and windows. A windows specific backup solution can use an external, USB connected, drive and work inside Parallels or natively in Bootcamp.
Finally, you shouldn't allow OSX to mess Windows filesystem nor the other way around, neither OSs nor their file systems are made with that possibility in mind.
Last edited: Dec 29, 2011