TheDaddy, should this be a new kind of minimig or "just" a new case?
If it is a complete new design and board, you are welcome to start a separate thread for it :-)
When I get my new PIC with tiny bootloader inside, I want to start testing and adding some features (e.g. write support in adf files) for the original minimig (Dennis' board).
A new design will make it impossible to test the same files because some wires or codes would be changed.
For other systems running "on" the minimig, the FPGA needs to know its hardware. Atari-ST custom chips or maybe Amstard CPC or C64 hardware has to be loaded into the FPGA via existing PIC or JTAG.
The PIC does not care what kind of "hardware" is going to upload into the FPGA. Once uploaded the FPGA will start its work and silulate/act as the loaded system.
Therefor the simulated system should "know" about the environment as the "Amiga" does. The same PIC also can provide .adf files for Atari-disk-files or big-D64 "adf" files for C64.
This is all theory now, but it can be done with knowledge of the emulated system and its behavior in accessing drives or external ports.