Just thought I'd take a minute to update this.
The Geo is finally (as of a couple weeks ago) running on a Contour ECU. No more terrible low rpm drivability that we had with the Mark VIII ECU. As for what can be removed, and still have the engine fully operable, you really don't need much. You need the ECU, engine harness, and a few wires for PATS. I feel like I'm now an expert on Contour wiring. We ended up building a custom harness.
If you're using internal PATS, you need a couple wires going to the key sensor. If you're using external PATS, you need the key sensor, PATS box, and the two CAN-BUS wires that connect the PATS box to the ECU. For internal, the key is paired to the ECU. Any key sensor will work. For external, the key is paired to the PATS box. The ECU doesn't care what key it is as long as it's paired to the PATS box. For this reason, we went with the external style PATS ECU.
We never did figure out how to get around PATS, so we just have a key duct taped to the key sensor.
