Is it probably the ECU?

The Dart's 360 with Holley double pumper was broken in and tuned using an MSD box on the dyno. When the engine was installed in the car with a Mopar orange box, it took us a little while to realize we needed to reset the timing because of the difference in the boxes. Got the engine running great with good throttle response. Took the car to the transmission shop on a trailer and it suddenly decided to begin having intermittent starting problems. For a quick fix, I tried a box from Autozone and it fired right up and has continued to every time since. However, now it has an initial stumble and sometimes pops through the carburetor on hard acceleration from standstill. Is it a timing issue, once again because of the different ECU?