this guy used the NISMO manifold to run ITBs with a KA24E-T setup:
http://home.att.net/~MabuhayCarlos/TurboStory.html
but for some reason his "fuel system" page is blank now. the last time i looked at it was a couple years ago, so i don't remember what he used.
when i got into bmw e30s, MegaSquirt was real popular. what a lot of guys did was leave the stock Motronic ECU in to run ignition, and then used MS, which is MAP-based, to get rid of the AFM. i think that's probably how i would go about it...
you *could* just enclose the ITB inlets in a plenum and have that pull through the hotwire-MAF, but given that ITBs are pretty much pointless if you're not running a hot cam, i think you're going to want some kind of programmable engine management (at least fuel, if not both fuel and ignition) to make the effort worthwhile.
my $.02