A small update.
I finally received my new 99xEIDE card.
I installed the "primary" CF on the primary IDE44 connector and a CD as master and a CF as slave on the secondary IDE40 connector.
At first I tried my old 99xEIDE drivers, simply since I had them in ADF and I could load them with the Gotek emulator... no results and I hanged the Amiga. 
I then used the NEW driver and now the CD is working and I have been able to install OS3.9!!!
And the issues I had with files loaded from the floppy (real floppy) now seem disappeared.
It's only strange that the preference program do see the second CF but I cannot see it working! 
And that I have some problems loading some OS3.9 programs...
More info to follow!
Thanks for the update!!!!