In addition to the dummy 68040.library and real 68060.library, you also need workbench.library. You can extract it from an image of Kickstart 3.1 for any other Amiga (it's not in the 4000T ROM). Space on the Install floppy is going to be tight, though. I'd suggest deleting expendable stuff (BRU) from a copy, adding the new files, booting from that, and then using the original/unmodified copy to run the install itself. Then copy the new files back to the hard disk manually.
The reason you need to use an unmodified disk to install is that the Installer will probably choke when it can't find whatever was removed from the other copy.
EDIT: Replacement phase5 files
here.