According to the
Rooting Procedure on the Wiki:
Completely formatting the READER partition using the eReader's builtin format function (See settings) might solve issues where the update package is not being recognized or the update simply isn't started.
This worked for me after having the same issues as you describe under 2, 3, 4 an 5! In the end, I just used the
standard Sony Firmware to unroot and then (re)rooted with
Rupor's Root Package.