Good news everybody, I have had some time over the last couple of days to work on this and I have a version of the application ready that should be compatible with the Kindle Touch. It hasn't been tested much because I don't have a touch but it works with the Clippings file uploaded by robertpolson.
The new program is attached and it requires Java 7 to run, If needed I can compile it again with Java 6 but I plan on using some Java 7 features in the future so best to upgrade now if you can.
To aid in the development of this program it would be great if people could send me a clippings file with the following:
If I have a file with all of these for each model and version of the kindle I can better test for problems. I don't need the actual data just the structure. If it wasn't for people like pop and robertpolson the application wouldn't be where it is now.
If there are any problems let me know I will do my best to address them and as usual if there are any feature requests post them and I'll get round to implementing them.