I am a bit lost here - since you were able to do full back up using my recovery package - you where in recovery mode!
You need to have proper SD card in your device in order to stay in recovery mode and connect to the device - otherwise recovery script simply reboots the device into normal mode, exactly as you are observing
ebook_msc is Windows program (created by igorsk and porkupan) which uses Sony proprietary protocol over USB to perform some actions (in this case force reboot into recovery mode), but it would not change anything if you do not have proper SD card - device will simply reboot into normal mode again.
In general in order to do "hacking" you are talking about you do not need recovery (and serial connection) - it is more than enough to use normal Android adb connection instead...