The difference with the A4000T was that it had the driver for the onboard SCSI in the Kickstart ROMs. But 'cos it was already pretty full, they had to make some space for the driver by moving the workbench.library out of the ROM and putting it onto disk instead.
OS3.5 and 3.9 updates that apply to different models of the Amiga are handled by SetPatch , it can figure out what Amiga it's running on and only apply the updates that it needs to load at boot, so there's no need to have different 3.5/3.9 discs for each model.
If you've got a working 3.1 installation, it should just be a simple matter of popping in the CD, and following the prompts from the installer.
