Update: Got serial to work. Tried the level converter, that didn't work for me. Used an arduino to read the serial - that works perfectly. Maybe my converter is dodgy. Stuck a socket on the chassis of my kindle so I can use the serial port all the time.
I have a question - If I have access to the serial port, is my kindle basically unbrickable? I ask this because I am doing all sorts of flashing to try to get android to boot and I don't want to toast my device.