It would be easier to flash with fastboot than writing a custom MfgTool profile.
Now there is a windows version of fastboot, but you need to install the libusb-win32 device drivers to use it. You can start fastboot mode in windows with MfgTool, then use the windows fastboot, with no risk of dropping out of fastboot mode when the USB port resets or drops when switching operating systems from windows to linux.
The "simple debricking" thread now has a downloadable linux kernel for the main partition, in the event that yours got damaged in the mmc. You can flash the main and diags linux kernels and the diags partition from fastboot, but you need to boot diags and use dd to flash the main partition.
If you *really* want to learn to use MfgTool to do new stuff, you should connect to the kindle serial port so you can see the status messages that result from commands sent to it by MfgTool.
I suggest that you first go back to the fastboot flashing method and try that, using the windows fastboot. There are posts that show how to install and configure windows libusb-win32 drivers. If you need any kernel or partition images not posted in the "simple debricking" first post, you can request them here or in that thread.
And do not worry about thread necromancy -- please use this thread for relevant content such as yours, and keep us posted about your progress (and MfgTool investigation).
Good luck, and good learning!
