I honestly wouldn't know about the majority of these issues (and, secretly, I suspect most universities don't either).
Aside from legal issues, it seems to me the business proposition is the same as the open-source business proposition: you know the most about the system you've created, so you're in the best position to consult on it. If you want a startup, I think guys like Cloudera show that even if you give away what was traditionally thought of as the family jewels, you can still very effectively monetize. That's what the university should leverage.
Anyway, for most projects, you've already given the game away in the paper (or at least, should have done): the expensive thing was the idea. Reimplementation is cheap.
I'm surprised that as a researcher you have not had notification or training about Bayh-Dole (someone mentioned they are in your lab so I assume you're funded). Universities have to report that they have notified researchers about the act. Here, all grad students have to sign an acknowledgement form indicating that fact during orientation. Flaunting the act has serious implications for the university's federal funding. It's government research privatization indoctrination 101 since the Regan revolution.
It's funny because the public (like you) demands access to the research because they paid for it, but the politicians view you as an economic investment and demand that you monetize and produce returns (e.g. tax revenue, employment from startups). The public doesn't write the rules.
Aside from legal issues, it seems to me the business proposition is the same as the open-source business proposition: you know the most about the system you've created, so you're in the best position to consult on it. If you want a startup, I think guys like Cloudera show that even if you give away what was traditionally thought of as the family jewels, you can still very effectively monetize. That's what the university should leverage.
Anyway, for most projects, you've already given the game away in the paper (or at least, should have done): the expensive thing was the idea. Reimplementation is cheap.