A) It's not still running anymore. The reset really killed the process. For sure.
B) if you can kill the framework safely then sobeit. Give that a try.
(requires launchpad installed IIRC)
C) you can try liberator again. no qualms there. Just reset if it freaks.
D) The kite folder will be when you extracted the zip. It can be safely deleted.
E) Huge pdf files kill kindles. Even the swanky new ones. You can either split the pdf into manageable chunks.
Or use a 3rd party thingy to resize/remungle it the way you want it BEFORE you read it on the device. Those are your choices.
Hope it helps