@folyjo: The Cli problem is a bit worrying. Since you have OS3.9, have you tried VNC Shell that comes with it? Can you use 'execute command' from the menu? Either way, I second the advice to both do a full virus check of your system, and to re-install /System/CLI ...
As for FBlit, well I never had that problem, but it did take some work getting it going. The first few times after installing it, my Amiga wouldn't boot.... be sure to read the docs very carefully.. Once you can find out what program(s) conflict with FBlit, you can set FBlit to not affect those programs, via the GUI.. (FBlit_GUI , IIRC)
Regarding WHDLoad... that 'Exception Access fault' error I have seen many times. Make sure you have the newest version of WHDLoad installed, and the newest version of the installer for that particular game... Some versions of some games just will not work on some systems, WHDLoad'ed or not...
I could never get my originals of MK2 installed....