Ignoring the technical side of things altogether, there's a more pragmatic way of choosing a simulation suite (or method of doing anything engine-related for that matter).
Do you use the tools that are recommended and used by the people designing and building 400+hp/liter engines professionally? Or do you use the same tools used by builders of <300hp/liter bikes? In other words if your advisor is building 60hp engines, you're unlikely to do much better using the same methods.
The development of two strokes has never stopped, even since the days of the Aprilia GP bikes. Look at the T/A figures we used to use in the old days and compare it to what's being used today - they're worlds apart, as are the outputs. But I think anyone interested in high output two strokes needs to be looking further than just bikes these days - much of the interesting stuff is being done with karts and snowmobiles.