Hi Corrado,

i would prefer travelling this route
a) Flensburg - Glückstadt (no specific cycling path here),
b) crossing in Glückstadt the Elbe with the ferry (allthough youre missing to visit Hamburg)
c) heading south from Wischhafen to Bremen
d) using the Weserradweg (http://weser-radweg.de/) along the river Weser
e) and then the Fuldaradweg (http://www.fuldaradweg.de) along the river Fulda
f) nearby Schlitz using the Vulkanradweg (http://www.vulkanradweg.de/neu-bahnradweg-hessen.html) from Schlitz to Hanau or Frankfurt
g) and finally from Frankfurt or Hanau along the river Main to the river Rhine, using the Rhine-Radweg upto Basel or whatever.

imho the Rhine-Radweg is ennoying - espacially the parts south of Karlsruhe until Freiburg.

hope that helps.
ciao Jürgen

edit:
you mentioned guides:
* publisher bikleline, Weserradweg,
* same publisher Fulda-Radweg
* same publisher Rhein-Radweg (Attention, there are 3 different ones, each handling different parts; you need No 2

The other parts i mentioned, i don't know a specific guide. Perhaps your familiar with "normal" maps, so the ADFC Radtourenkarten will help you. The Vukanradweg-Trail is easy to handle w/o a map, i guess. It's just an abandonned Railtrail, now an asphalt street like a small ribbon alongside and over the Vogelsberg (easy to ride allthough climbing up).