An updated version of MiniMig 2 would be a good idea:
1. Use the ARM-controller by Yaqube along with the ARM Reflash USB connector.
2. Use 4MB SRAM (QTY=2 of CY7C10612DV33=> 2 x 1Megx16 )
3. Since FPGA is out of I/O, you could include a small Xilinx CPLD & some transceivers (74LCX16245) on 68K bus to add a real IDE interface with A600/Gayle register set & 44pin IDE connector.
4. Connector with 68K bus on it.