had to remove the HD Toolbox and all the languages except English to make room for it
Hope you did that to a backup copy...
It's SetPatch that makes an 060 Guru if the libs aren't installed. What you can do to skip it is boot from the floppy without startup-sequence, assign ENV: to RAM:, run LoadWB, and then run the Installer from the cut-down system.
When it tries to reboot the machine, copy the dummy 68040.library and the 68060.library to Libs:. Then let it reboot. It should boot right back up to a normal system.
If workbench.library is still somehow missing, you can pull it out of another (non-4000T) 3.1 ROM image with RomSplit/Remus.