Is it probably the ECU?

Based on the symptoms it could be either carb or ignition. But I would certainly look at ignition since that is the last thing you changed....

If ignition related: It is perhaps the timing; that is an easy enough thing to check, right? Is this happening at all RPM's or just low or high RPM's? Otherwise, it sounds as if the spark may be getting weak per the symptoms. Could be the box, the coil, the coil wire, spark plugs or plug wires, rotor, distributor cap.

What coil are you using?

BTW, when you originally changed timing for the orange box, how much did you have to change it from the MSD setting? It would be no surprise at all for there to be timing differences, based on circuitry differences. They could easily have different internal delays or even trigger off opposite edges of the pickup pulse.

Any way that you could have flipped the polarity of the pickup connector on the distributor when you installed the orange box or the new box?