5V to 3.3V bus and vice versa

Just to clarify; the problem is that the MC68000 input threshold voltages are 5V HCMOS compatible, but not 3.3V compatible?

You could use two buffers; a bus switch between the MC68000 bus, so that the Cyclone II device sees 3.3V signals, and then a 5V buffer from the Cyclone II to the MC68000. When the MC68000 performs a bus access that corresponds to the Cyclone II, the bus switch will route the control signals from the MC68000 to the FPGA, and then the Cyclone II can drive the response via the 5V buffer (which would have 3.3V compatible inputs).

Cheers,

Dave