Just a thought guys (and gals?)
Most of the old Atari custom chips could be easily implimented with some of the smaller FPGA chips (I'm fairly certain even a low end Xilinx Spartan could do the trick). I would imagine that a working ST, a scope and a good VHDL coder should do the trick.
You'll get close to hardware compatibility, and be done. Heck, you could even load different fpga configuarations to let you emulate different ST hardware revs.