These are a lot of questions. I'll start at the highest level, which is why are we behind in innovation.
Lots of studies--including one from the Council of Canadian Academies--believe the problem is mainly in business innovation; that is, management making the right decisions to advance their business. That has to do with all sorts of things, including where you invest your dollars, getting state-of-the-art information, application of new technologies, tools for the industry. The biggest problem is not with R and D but with these other factors.