Ok, I could fix the problem with flashing of the Fairphone binaries via SP Flash Tool, see here:
http://forum.xda-developers.com/wiki/Fairphone_Fairphone/Guides#How_to_restore_Fairphone_if_you_totally_bricked_it
For this I needed a lot of time to find all tools and drivers for download. If somebody needs all the files, please contact me with a personal message so I can send you a download-file with all needed drivers and tools.
I used Windows 8 to flash the binaries. After flashing I could install the Google Apps and now I’m installing all my apps and restoring the data…
Please note: I did the manual update before with formatting the phone to get the new storages. After that I couldn’t reinstall the Google Apps.