After all this time I finally dared to do this last step.
All my harddisk was messed up, but it was only that partition #1 was suddenly starting at cylinder 3 in stead of 2. After fixing this and having SFS loaded in HDToolBox everything went fine and I was able to copy over all partitions from both my harddisks to my new IDE > CF 8GB Microdrives.
Currently I'm waiting for a better IDE > CF converter, as mine i a double one but only contains 1 slot, so I can not hook up 2 at the same time.
So Thomas thanks a lot, I'm happily Amiga'ing again.