The hundreds of hours of reverse engineering and fiddling that is required to hack a stock ecu (and deal with it's limitations), it's more cost effective to buy an aftermarket ECU and develop your own tune for it. I'm suprised no one has grabbed a MS3PRO Module, slapped down a custom 2GR PCB with connector for it and pushed it out for sale as a drop in, plug and play ecu.... Could even put it in a factory case :)
http://www.diyautotune.com/ms3pro_module/index.html