if you need an intermediary step, the ITBs can breathe through the AFM. this is how my car is set up right now, and it's working well enough that i'm not really anxious to go megasquirt yet.
if you are dead-set on getting rid of the AFM, you can try the hardware dbilas uses for this purpose- "alpha-N 2000". piggyback computer that takes TPS/RPM and feeds voltage to the AFM wire based on those. mine was DOA, but i got it used, so you might have better luck. other than that, your good option is... call dynotech and get a PnPMS.
but with the complexity of the task you already have at hand, i honestly would leave the motronic alone (excepting get a MarkD chip if you haven't already) for the moment. get the ITB setup working with that and you'll know it's solid when you want to move on to better management later. doing ITBs and new engine management at once introduces many variables and is going to make troubleshooting and tuning more difficult.
my $.04- good luck.