Learn English – How to punctuate a quoted rhetorical interrogative sentence that ends a declarative sentence

My answer is not really in the other threads except partially in the comments from programmers, so here goes. First, instead of looking for a single correct way to do things, I think it's more helpful to think about what is acceptable and understandable to your audience. Your real-world experience will more effective and less confusing this way because different audiences have different expectations and conventions.

Below are a few variations that I find acceptable and understandable, with notes on the type of audience that I think they best fit. Your original paragraph was understandable and possibly good for people who like smooth-flowing text that reads a lot like speech. But I think it could also use more-informative capitalization and punctuation to clarify the structure for others. I added these changes in the first example, in case they're useful.

1) Those of you without any experience with drug or alcohol addiction are probably reading this scratching your heads thinking:

"WTF is this guy talking about? If their problem is not drugs or alcohol, how can they be classified as an addict or an alcoholic? And why do they consistently abuse drugs or alcohol? How is that not their problem when they can't hold down a job or take their kids to school because they're always under the influence?" [scientists, mathematicians]

2) Those of you...thinking "WTF...the influence?". [programmers]

3) Those of you...thinking, "WTF...the influence?" [people who read English prescriptive grammar books (whether they are grammar snobs or perfectly nice people seeking the knowledge or opinion of other language users)]

Also, I'm very curious why you put those first two commas there. Do you pause when you say the sentence there, or were you thinking about the sentence structurally? I'm just curious.

Edit to add examples for suspect advice. As far as I know, you cannot search for punctuation on google because they ignore it. However, there are some search engines that intentionally include punctuation, and they luckily happen to be aimed at programmers. Here are the results from a search for ?"., which got 247 hits. Interestingly, most of them appear to be from SO (StackOverflow, a Q&A site for programmers). Some examples:

1. I asked the question "Will Rebol 3 extension support any windows api call including those requiring callback ?".
2. None of these answers address what I understand to be the question, which is what I was searching for, "how do I handle items that have visibility == hidden?".
3. Question was "How can I then find out the application running time ?".

For comparison, a search for ?" gets 5,258 hits (trying to include a terminal space made no difference). However, here are some examples showing that this returns lots of what in our case are false-positives since the quote doesn't end the sentence:

1. How to detect “has user selected entire document or not ?” in html javascript
2. Bind collection as the right-hand-side of a “where col in ?” clause
3. Our project application uses Java 5 and now when I update Java 6, there are some kind of inconsistency with functionality and seeing this effects our manager passed comment that "Java is platform independent but version dependent", Is it really true ?

This last example is notable because they use the comma outside of the quotes, but the title is Is it correct to say that “Java is platform independent but version dependent ?”. So it's not always obvious what people are thinking.

Wikipedia also notes this "logical" style, though in connection with the UK and "science and technical publications".