Covering half the maf?!
If you are running it without an airfilter it will not get consistent airflow across the sensor and it will be inaccurate. Filter smooths the airflow. Hand is not quite as consistent..
Sorry if I missed this.... did you reset the pcm after replacing various parts. If there was a problem with one of the misc sensors, specially the maf sensor, the adaptive learning may have been skeewed to it's limits. It would eventually relearn but its quicker to start from the base settings.
Just curious...will it start and idle smoothly if you disconnect the maf sensor?? It will default to the failed mass air table which relies on throttle position and rpms. Its a limp home mode for failed mass air sensor. When its initially started it ignores the maf anyways.
If it idles smoothly and consistent I would suspect the mass air sensor/ circuit or vacuum leak. Only because you removed the maf from the equation. If not it proves nothing.... Just my theory