Does it show as a USB drive when you reboot the kindle? Can you boot to diags by putting an ENABLE_DIAGS file on it? If so, you can set fastboot mode from the diags exit menu (install fastboot bundle). Then you can get to fastboot without MfgTool and its driver issues.
And there is the i
mx_usb_downloader program that
ixtab mentioned, but you need to compile that from source code (or is there a binary somewhere?).