damn, good job on the work so far. you say you get 4.4K ohms at WOT but the FSM says it should be at 5K ohms +/-1K ohms but that may still be causing the stumble. This is assuming you have an S4 since you didn't mention narrow or full range (If not then you're off from the 6Kohms specs).
Have you double checked to make sure the fuel pump is getting full voltage?
IS your timing off? You say you have the wrong pulley, does this mean the marks are off? Have you set the motor to TDC and remarked the pulley?
Your secondary injectors are electrically within specs, is it possible that they're clogged though? It's a long shot but who knows.
It IS possible that you're just flooding the car when the secondaries come on. It only happens when idleing, right?
Good luck man. I'll think about it and see if I have more questions or ideas.