This is quite cool.
The benifits of hacking the ECU over just putting on a PCIII is that with the correct software you can adjust everything the ECU controlls, not just adding some fuel as needed like the PCIII does. You could adjust the spark advance, add (or remove) fuel as needed, and I imagine adjust the idle and the opening of the secondary butterflys.
Of course, in addition to hacking the computers you would need to add, or adapt, software to modify the programming.
This is what the Buell guys do to their bikes since a PCIII will not work, but they get to adjust the spark map, the fueling, cold start enrichment, etc.
Of course this is a big undertaking, and since there has been little work done on it to date (at least it sounds like it) a better step might be to switch to MegaSquirt ( www.msefi.com
). MS basically allows you to control the fuel and spark for dang near any engine, heck you can build the fuel and spark systems from scratch and control it. Plus, it's fairly cheap (~$500).