Good news. Assembly is the right way to do I think.
I had to code my own MFM routine in assembly in order not to loose every precious cycle, of which there hadn’t been many.
Now the MFM part of my project is complete, I’m struggling with the rest – interfacing with DRAM (old 1 Megabyte SIMM for storing the whole floppy image), reading MMC card (and FAT16 in particular), dealing with LCD and buttons etc. I will also have to switch to a more advanced MCU (24 more IO lines to interface with Amiga’s floppy bus, and probably to deal with real floppy in the future, to be able to read/write floppies to/from images on an MMC card).