Well well well :-)
Since some times now (don't remeber how long ;-) ), there is NO NEEDS for a dummy 68040.library anymore!
Setpatch WILL look what library is installed in LIBS: and then load the one it finds.
So you just have to install the library you need in LIBS: in your case I would recommand the 68060.library from the MMULib latest package (v43.6), AND the MMU.library itself (use the mmulib install script for that).
Don't forget to verify if the 68060 caches are on as without it the 060 will CRAWL :-)
Hope this help ;-)
Amigalement,
Jean-François, Amiga ONLY since 1985.