I would also be interested in reading that thesis. I was thinking a while ago that going to grad school to work on something like that would be cool.

One thing that occurred to me is that shifting focus may work better as a gradual activation than an immediate one. In other words, focus would be an average of eye position over time, and after reaching a certain threshold on a certain element, the focus would shift.

Not sure it would work in practice, but perhaps it could ameliorate the chaotic effects you were mentioning.