I don't have any 68040.library at all.
I tried the Commodore 68040.library from the 3.9 disk and my Amiga refuses to boot also, which must have been why I didn't have one installed.
However, I don't have any apparent side effects from not having it. Sysinfo reports a speed of 17613, all apps and WHDLoad games work.
I'll see if I can round up a working library tho.