Bart,
It sounds like everything is functioning properly. If you have no codes then I would think it is either the tune or it is mechanical. It should be fairly easy to try a different pcm, even with a stock tune, you could make a determination about you stumble.
If you use the stock tune on you motor you obviously don't want to hammer on the car too bad. The knock sensor would pull timing and keep you from melting a piston but still use some restraint.
I had a similar issue for a while at high rpms. At 5200 the car would fall on its face. Turned out to be valve float. Easy fix but I'm a slow learner and it took a while for me to figure it out.
One other thought, I remember when I started my swap, some guys were already using the mass air equiped cars and were having problems with stumblling caused by turbulance at the mass air sensor. I'm not sure what you,ve got from you filter to the sensor but you may want to try a few different configurations of ducting to the mass air sensor. If I remember correctly, the problems was related to the air taking a sharp turn just before the sensor.
Good luck. The offer stands.