have you looked on the duccutters site?
There's at least one superbike running a 2V engine
http://www.duccutters.com/Hull-944Corsa.tpl - may be more as well, I haven't looked for a while.
Having had an MTS1000 and an ST2 I wouldn't say either engine is ideal - both a bit flat for track use, but you could definitely ride the wheels off them which seems to be the goal.
I think you'll have inlet clearance issues with the either engine - I'm thinking of going the other way (916 engine into my MTS) and putting them side by side the frames are quite different around the inlets, and the 916 intakes seem to go through where the bracing is on the MTS frame.
If you're doing all this you could consider chopping out the bracing where it gets in the way and refabricating a 2V style brace, but don't position it so that it feeds loads into the middle of an unbraced tube.
Mark