I updated clover through the update button of clover configurator, I updated FakeSMC the same way. After that I used the terminal to update apfs.efi with the following command:
sudo perl -i -pe 's|\x00\x74\x07\xb8\xff\xff|\x00\x90\x90\xb8\xff\xff|sg' /Volumes/EFI/EFI/CLOVER/drivers64UEFI/apfs.efi
Then I downloaded Mojave and launched the update.
All went fine, USB ports working, Camera and Apogee One working, nothing broken at first sight.
But later I discovered a problem with Preview crashing on me when opening some formats like jpeg.
I thought that maybe the RX480 was the culprit so I tried to inject ATI in clover, I tried lilu kext and Whatever green but it didn't help.
Finally, I activated my iGPU, the HD4600 in the bios (Asus board) to be active as a secondary GPU and added Inject Intel to the clover rules.
Now preview doesn't go in a endless loop anymore and I still have full GPU acceleration without any ATI Inject, or extra kexts.
Only problem now is that some Auto-play websites crash Safari, just like it does when running my computer without an eGPU.
Those websites I open with Chrome.
I can see a 137.89fps in Cinebench OpenGL and 133728 in Geekbench OpenCL Score.
Finally, I am gonna use the occasion of this post to say a word about moving from a GTX1070 to a RX480, which has been both a blast and a revelation.
The RX card is technically slower than the Nvidia card by a large margin, still the RX card scored better in Cinebench and was only slightly slower in Open CL. I couldn't believe my eyes, just moving windows around and opening/closing apps on desktop, everything felt smoother, snappier and prettier. Even my girlfriend, who's often borred by technology, noticed in ours streams on a large TV used as second screen, that everything felt more vivid and sharp.
By the way, I am using system definition 14,2.
Thank to Tonymac and all the community for your dedication, I always find in the forums the informations I am after.