There really isn't a solution for the AFM outside of just running a standalone. There is of course a MAF conversion, but bmwman91 worked on it for quite a long time and could never get it exactly right. And not to put a damper on your pursuit for more power, but Metric Mechanic run stock throttle bodies on their 210bhp rally motors. I can't imagine it being that restrictive, though not indicative of throttle response they do have quite a large surface area at WOT.
Maybe rather than trying to force more air into your motor by cutting your airbox in half, you should install an adjustable fuel reg and dial down the fuel pressure a tad.