Summary: So, you're saying (1) Taubes is indeed prone to confirmation bias, as he pushes his Big Idea too far; and (2) Taubes isn't a contrarian when it comes to cold fusion?
Disagreement: While Taubes may have been seduced by his Big Idea (as I wrote in the OP), I'm not sure the data you've cited are strong evidence of that. You've cited his "spending a lot of time defending those statements rather than reinforcing the more likely factual parts." But perhaps the "more likely factual parts" don't need so vigorous a defense because many people find them plausible already. Thus he spends more time on the parts many people find implausible.
This is evidence of confirmation bias, but I don't think it's very strong.
Have I understood your point correctly?
Here is the link. The context is nutritional science and epidemiology, but confirmation bias is the primary theme pumping throughout the discussion. Gary Taubes has gained a reputation for contrarianism.* According to Taubes, the current nutritional paradigm (fat is bad, exercise is good, carbs are OK) does not deserve high credibility.
Roberts brings up the role of identity in perpetuating confirmation bias--a hypothesis has become part of you, so it has become that much harder to countenance contrary evidence. In this context they also talk about theism (Roberts is Jewish, while Taubes is an atheist). And, the program being EconTalk, Roberts draws analogies with economics.
*Sometime between 45 and 50 minutes in, Roberts points out that given this reputation, Taubes is susceptible to belief distortion as well:
I do not think Taubes gives a direct answer.