Supercharged,
I owe you an apology for my remark. I'm sorry. Too many hours at work and I come home to the forum and I'm in attack mode. Shame on me.
Anyway, I'd be curious to see if you can pass smog with the aftermarket engine management. As you indicated, you can adjust a/f but I would think that the egr valve operation would present a potential problem. With the stock ECU, the egr position is both controlled AND monitored. So, for example, if you try to bypass the egr, the ecu will toss a fault code... a sure way to fail the test. In your scenario, you have the luxury of mankeying with the EGR without the fault code.
Anyway, your experiences in trying to pass smog are both welcomed and appreciated. I for one, am hungry to learn more options. (My only original point is that the new reader here should not be misled to believe that he/she can control a/f with anything short of a replacement of engine management electronics.)