"Givewell’s defends their use of DALYs by citing that they are commonly used."
The post you link to is from 2008 - 9 years ago. GiveWell subsequently became somewhat disillusioned with DALYs (see http://www.givewell.org/research/DALY) and has developed their own models of the ultimate effects on human welfare of a variety of different benefit flows from AMF, deworming and cash transfers. For example, you can see their cost-effective analysis for 2017 here (http://www.givewell.org/how-we-work/our-criteria/cost-effectiveness/cost-effectiveness-models) which I think is closer to what you're looking for.
Even on the page you link, Holden says of DALYs: "It is also true that we personally find the metric to be unhelpful."
"They erroneously (or hyperbolically) identify that they are identical to QALYs."
I can't see anyone from GiveWell saying this on the pages you linked (though perhaps they do somewhere else). You may be referring to a comment from 'Ron' who mentions "the essentially identical metric of QALYs" - but Ron is a random commenter who is not associated with GiveWell.
I suspect a post critiquing GiveWell will have to cover a smaller range of issues, with substantial care applied to each one, in order to help them do better.
I think "red teaming" GiveWell (or other people aiming to do good) is a great idea and I encourage more people to try it. However, I think this critique aims a bit too broadly and shallowly and misses a lot of the detail. Generally speaking, GiveWell has put a lot of time and effort into their thoughts and are generally unlikely to be overturned by a few hours of thought.
I'm not here to "defend" GiveWell. I think GiveWell is a very sold, thoughtful organization, though they are capable of making mistakes (indeed, they openly list some). However, I think your analysis of GiveWell is woefully incomplete and would benefit from a lot more depth.
I've left individual comments here about what I think you've gotten wrong.