The procedure I used to install Workbench 3.1 was to make a custom boot disk with the O60 libs and workbench.library from a copy if the standard WB3.1 install disk. I had to remove quite a few of the install files to make room for it. You won't need the 060 libs but you will still need to delete some files. Once I booted the A4000T from that floppy, I removed it and inserted the full WB3.1 Install disk, did the complete installation, and reinserted the custom boot disk at the end and manually copied the workbench.library and 060 library files to the Libs directory.
There must have been a special set of install disks for the A4000T but I have no idea where to look for them.