Let's see - two computers, three power stages and two coils, and it still stops running when the car gets to operating temperature. Unplugging and re-plugging the power stage connector often cures the problem.

There are only two other possibilities, the hall sensor and the wiring. And I'd suspect the wiring, and specifically, the connector at the power stage plug or the wiring leading out of it. One possible scenario - a break inside the plug or the insulation involving the ground, for example, would create the symptoms you describe. As the engine compartment heats up, the insulation relaxes, the wire slightly separates, and arcing causes poor running, and eventually, a full break. When you pull the plug, the wire moves, and re-connects. Till the next time.

Also could be the ground connection itself.

Could be the hall, but I can't imagine how that would correct itself by unplugging the power stage connection.