Whew! This is beginning to sound like a LOT of work. Don't worry, there's a lot of text here, but once you understand the problem it's not that hard. The first thing you should do is make sure that you completely understand the way Triscuit executes instructions. Do each instruction by hand pretending you are the state machine just to make sure you understand the sequence of things that has to happen. Once you understand this, it's just a matter of state machine design and you know how to do that (plus hooking up a few other components like counters and registers, but you know how to do that too). The nice thing is that once you have the circuit working in Viewsim, you don't have to do much wiring. Most of the wiring is contained in the Xilinx FPGA. Of course, there is a little wiring left to do, mostly in switches and lights.
You should also make sure to fix the external signals of the Xilinx part to specific pins and keep them there. Once you wire everything up, you may discover problems and have to fix something and try again. If you've fixed the pins, this requires only reprogramming an EPROM. If you haven't, it will require re-wiring!
Since there are extra Xilinx pins and extra bus wires anything else you want to include is up to you. What are some things that you might want to consider? You might want to include lights on the state bits for the state machine for example. Any other signals that you think might be interesting to see, you might want to bring out to pins of the Xilinx part so you can see them.