Sorry to hear it got worse.
As MD5 is checked against the *.img in /tmp/self_update/ you will have to copy this file back to IM (/Data/), obviously using a different name as kartu wrote.
You might also want to capture and copy back the output of the MD5 command /usr/bin/md5sum $TMP_IMG
Regarding the Software versions:
One of the hacks in Hack300Update is to "tell" the PC-Software that it is installing version 1.6.00.18040, which is higher then any actually released fw-ver, and so allow flashing.
But the fw-images flashed are version 1.1.00.xxx. That way Hack300Update can be applied as often as necessary.
Holding my fingers cross that you can re-establish access to the drives.
One last thought:
For my 505 there is a difference if the reader is restarted with the USB cord already connected, or if the cord is plugged in shortly (within 1 second) after flipping the power-switch.
With the later method the drives will show up more reliable.