I believe this may be a little bit tricky to determine since you are not using Yocto. Nevertheless, could you share with us the files found under boot/?
Actually not all files are needed. With firmware 1.0.4 installed following files on SD card allows to boot:
│ └── boot
│ ├── bootia32.efi
│ └── grub.cfg
where bootia32.efi is a grub built from sources with multiboot option to load my custom kernel. All files except kernel I may attach since they are open source. I just could not find attach button
I found a problem myself. The reason is with EDKII UEFI BIOS. It actually loads grub from SD card. I replaced EDKII with verion 1.0.2 and made a link
Quark_EDKII -> Quark_EDKII_v1.0.2
After that I am able again to boot from SD card.