Don't believe it will fit Crunchy. Ignoring for a minute that they are very different engine/injection systems, the 916 has the ECU box mounted under the seat and the 996R - like all the Testastrettas - has the ECU mounted next to the battery under the right hand side fairing. It's a completely different design. Why do you want to change the ECUs over?
The 996R ecu is the 5.9M type and as I see it offers no advantage over the 1.6M ECU fitted to the 916, if you wanted to fit the 996R ECU there are a few bits you would need to change, the main harness is different as is the front harness and the pressure sensor and Temp sensors. The 996R also uses shower injectors which I presume dictate a big difference in the fuel map. There are a variaty of different chips for the 916's ECU some that work better than others and there is also the fitting of a Power Comander to be considered.