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….. 
Be aware that the new Kickstart 3.1.4 contains battmem.resource and battclock.resource that are not compatible with Amithlon. Your system will no longer be able to save time and will revert to 12:00 AM, January 1, 1978 on every boot/reboot.
The only way around this is to build your own 3.1.4 kickstart with those files removed from the ROM and allow Amithlon to inject it’s own (that are also stored in bigird.gz/smallird.gz along with the kickstart “shape.rom”).
Hi,
any tuto to do it ?
No tutorial yet. It’s tricky as you’ll need an Amiga/Amithlon setup to put it together. I used WinUAE to install 3.1.4 to an A2000 based WinUAE setup. I then compressed all the files into an .lha and moved it over to my Amithlon system and extracted it to a new partition I created. I then started going through my Amithlon sys: volume and grabbing all the files called in the Startup-sequence, User-Startup, C:\AmithlonC folder, S:\Amithlon_patches folder, monitor files in Devs:, etc… and made sure the 3.1.4 system had those files in place. Grab anything related to Amithlon (devs/libs/S:/C:/etc…. that is specific to your booting Amithlon. Set that partition as bootable and then powered off (to flush out the 3.9 setpatch loaded modules, etc..) and powered on Amithlon. Caught it on boot with both mouse buttons and selected the new partition to boot. I also disabled the 3.9 boot partition. You may have to do this numerous times until you have a fully functional 3.1.4 boot system. You can then uncheck bootable for your Amithlon’s 3.9 boot partition. You’ll have to eventually create a 3.1.4.1 kickstart ROM for Amithlon and embed it in the smallird.gz file you launch Amithlon with.
As for a tutorial on making your own Kickstart or embedding it in smallird.gz, I haven’t even considered writing up one but I may have to do that. Create the ROM same as you would for creating one for an Amiga, just use the Amithlon battmem.resource and battclock.resource, the 3.1.4 ones will not allow Amithlon to save the time/date and will always boot up/reboot to 12:00 AM, January 1, 1978.
Pedro Cotter wrote a quick guide on how to easily replace the embedded Kickstart in smallird.gz with your own. I may have to add that process to my guides when I update them.