The amidock problem is defenatly a lib one.
Make sure you have the 040dummy library installed as 68040.library. It's size should be a lot less than the 68060.library. AmigaOS doesnt know about a 060 library, so it reads the dummy one which then goes to read from the 060.
Also make sure that you dont install 060 versions of apps, since they expect a full 060.
I'm not on my miggy right now, but I could give you my versions and sizes when I get home.