I haven't read through the whole thread, but right now you still having the car stumble. Have you determined what you are losing when this happens? ie. You need fuel, spark and compression. Starting with the assumption that you are not losing compression (ie. valve hanging open.) That leaves fuel and spark.

Fuel: a fuel pump failing will behave similar to what you describe. Fuel pressure gauge hooked up will tell you that. Bad injector driver/wiring harness issue could cause something similar. Wiring (backprobing or piercing probe) a light in you can see if there is complete failure. Oscilloscope would show sporadic issues. If it is a wiring harness issue, you might be able to press on the harness lightly and get it to happen at idle...

Spark: Again you could wire in some test lights and see if power to the spark or ground side switching goes away.

Once you figure out what is going away, you can determine the why it is going away...