Just booted the system off the latest Kickstart 3.1.4 and Workbench 3.1.4. Definitely a bit of effort involved but it works.
I replaced the kickstart in smallird.gz with the A2000 3.1.4 Kickstart and installed WB 3.1.4 in WinUAE to give me the files for setting it up on a partition in Amithlon. Compressing the new sys: partition to an .lha and then uncompressing that on a volume on my Amithlon I was able to boot off Kickstart 3.1.4 and Workbench 3.1.4. I will continue to experiment with it and see how it compares with 3.9. I have a lot to setup/configure still…..