Well barry as a scientist you should be pleased, because there now appear to be 2 independent and fairly serious attempts to test your hypothesis concerning gyroscopic and other effects of the L4 engine configuration on vibration and handling, the hypothesis not necessarily being without merit in my inexpert opinion.
Ducati corse would appear to be trying to solve their bike problems by chassis re-design +/- engine re-positioning without ditching the L4 engine; first impressions were positive with the bike looking much better and able to be ridden in a conventional manner at a competitive pace, albeit with jumkie's caveats that the pace may not have been as competitive if normal circumstances, and in particular the involvement of the 2 factory honda riders, had applied.
It would also apeear that honda, with the odd engineer in their employ with a passable record for engine design (which doesn't preclude them being wrong in this instance of course), are going L4 for at least a road bike and possible a wsbk.