The PDFs may be a problem. If they are mostly text, they can be converted for use on the Kindle and will work well. If they have a lot of charts, graphs or tables, you will not be happy with the results. As AnemicOak mentioned you'd better off with an iRex iLiad.
Check out this
help file page for the Kindle 2 which explains how highlighting and saving clippings works.
Quote:
Editing the "My Clippings" File
All of your bookmarks, highlights, notes, and clippings are stored in the "My Clippings" TXT file on your Kindle. You can transfer and copy the file to share and use your clippings.
To transfer the "My Clippings" file and open it on your computer:
1. Connect your Kindle to your computer using the USB cable.
2. Use your computer's file browser to view the Documents folder on Kindle.
3. Transfer the "My Clippings" file from Kindle to your computer.
4. Open the "My Clippings" file on your computer using an application that can read or import a .txt file.
If you wish, you can make changes to the file and transfer it back to your Kindle. Changing your "My Clippings" file does not affect any notes, bookmarks, or highlights you've made in the actual content. The next time you read the content, you can still use them for navigation and reference.
To remove the "My Clippings" file from your Kindle:
1. Press the Home button to display the Home screen.
2. Underline "My Clippings" on the Home screen.
3. Move the 5-way controller to the left.
4. Press the 5-way to select "Delete."
Kindle adds a new "My Clippings" file the next time you add a clipping or annotation to any content.
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Since you can copy the "My Clipping" text file to your computer, you can convert it to a PDF if you prefer or just about any other format you like.