Interesting take on arguments, but the guy is wrong about for example - the logic of spending money to prevent rare causes of death. The problem is that prevent common causes of death usually fall into the class of wicked problems. This is actually a point that the author raises in the rebuttle, when he says, "Unfortunately, running a government or an economy is a little more complicated, and we're still stuck in "Bear = Run Away" mode." This same point can be used to argue that, for example, it would be cheaper per death prevented to try to stop deaths by bears - even though these are statistically rare - than it would be to for example, stop deaths from household accidents like slips and fall (which are far more common). How you attack the problem of stopping deaths from bears (shoot bears) is conceptually easier and more straight forward than actually injury proofing everyone's homes - to say nothing of being actually less intrusive (most people don't live with bears). This in no way shows that killing bears is money well spent, but does expose that there may be more logic in the argument than merely failure to understand probabilities. The logic may actually be, "This event is unlikely, but at least the answer seems tractable. Whereas I don't even have a clue about what to do about this more immediate and likely problem, so I'll have to ignore it whether I want to or not." The ultimate example of this is the problem of old age, which is 100% likely to kill you if nothing else will, but may not necessarily be worth spending a lot of money on right a way because there may not be any thing we can do about it no matter how much money we spend.
There are actually two other related common sense falacies tied up with that. One of them is the 'man hour' falacy, which basically says that if a problem requires 10 years to figure out, that if you hired twice as many people to work on it that it would necessarily require only 5 years to figure out and so forth. So if you spent 1000 times as much on a problem that took 10 years to figure out, you could get it done in 3 or 4 days, right? The answer is, not necessarily and indeed, usually not. Related to this in American discourse is the 'Manhattan Project' falacy, which says, that for any seemingly hard and intractable project, an answer could be readily supplied if only enough will existed to accomplish it. The problem with this falacy is that at the beginning of the Manhattan Project, science and engineering of building an atomic weapon were actually well understood. We had a pretty good idea of how to actually go about it, the math was worked out, and worse come to worse we knew of a brute force approach to the problem that would eventually solve it. In general, none of these are generally true about wicked and intractable problems, so comparing for example solving the energy crisis or building a car that runs on water to the Manhattan Project is generally a sign of poor education in engineering more than it is anything else.
Or in short, while there is no doubt that we mismanage our priorities, it is certainly not true that merely looking at the likelihood of events and other simple statistical would result in proper prioritizing. Indeed, as far as I can tell, the author in the second section is using some logical fallacies to insist on the logic of some of his own pet causes. One sign of this is that he's actually pretty admirably biased in attacking both sides of a political position in every other section, but trivially dismisses a series of related political positions in this one section only. This is a clear indication to me that at least in this section he'd stop thinking, "How do I show we are all biased?", and started thinking, "Aha, this is how I can win an argument!"
As for #3, I don't think I've ever thought anyone was being intentionally dishonest. In fact, I more often see the issues he raises in #3 being used as a fall back position as a way of dealing with uncomfortable facts. That is to say, when presented with facts, there is a tendency to cite sincerity of belief as a defence against truth either in the form of, "I sincerely believe X, therefore my opinion is just as valid as yours.", or else, "Even though you have evidence, your point can be dismissed because it associates something I like with something I don't want it associated with, therefore its ad hominem and you aren't allowed to point it out." Or in short, even though its probably true that no one in the debate is being intentionally dishonest, even if both sides know that it is not any help. The honesty and sincerity itself can be used as the basis of logical fallacies.