I am afraid I fundamentally disagree with... well, not all of that, but quite a lot here.

As we develop and mature I believe our cortical/thalamic complex gradually creates a VR type experience for our awareness, so gradually we no longer see what arrives at our eyes but rather is what is constructed from the direct sensory experience in the occipital lobe of the cortex - our visual center.

I see that differently. As I understand it, I would define "seeing" as activity in the occipital lobe. You see things in your dreams. When you do (AFAIK), that is because your visual cortex is doing things. When your visual cortex is not doing things? You see nothing. Thus "seeing" is that activity.

By the time we are adults our awareness can no longer directly perceive the external world.

We can never directly perceive the external world. And never could. How would we? This is one of those assumptions I really dislike.

To put it in Buddhist terminology: All of perception goes through the six sense doors. There is nothing that can be perceived that can ever or will ever bypass those. That is always all there is. There is no space for direct perception of the outside world. The only thing that can happen is that the mental faculty calms down, and that there is less of "thinking overlay" over sense perception. But all of perception is still fundamentally constructed, made, and indirect. Something that comes through a door, that can open or close.

If there can be that much variation between a practice based on the Theravāda commentarial tradition vs a practice based on the Pali Nikāyas, then how much change could have occurred between the time of the Nikāyas to the present day?

Okay, so we are talking about the Jhanas. And we are talking about the hypothesis that what is described in the Pali Nikayas is significantly different from the practice instructions you would arrive at by reading the old texts in combination with the Theravada commentaries.

Whatever the historical truth behind that is, this divergence plays out practically: You have Leigh Braisington (and previously Ayya Khema) practicing "shallow" sutta Jhanas. And then you have the Pa Auk school practicing the very deep Jhanas from the commentaries.

The point is that both varieties of practice are possible, and that the nature of the conflict is one of historical accuracy: "What did the historical Buddha mean? What kind of practice did he really advocate?", is the question people quarrel about.

Perhaps the experience of the jhanas is different today and maybe we should be looking at the jhanas differently than did the Nikayas or Theravadens.

The thing is: It doesn't seem like that. The descriptions of the "shallow" Jhanas in the suttas are still accurate. That I can say from first hand experience. And from what I hear, the commentary literature which describes the deeper Jhanas with nimitta also seems to reflect the experiences that occur very accurately.

The only conflicts we have in regard to the Jhanas are conflicts about historical meaning, and historical validity in context with a Buddhist canon: "What did the Buddha really teach?", is the main question people are arguing about. "Do the descriptions fit the experiences?", is not a question that regularly comes up, because usually they fit very well.

The way our cortex is ultimately wired and the way our senses become mapped to our external world is affected greatly by the culture in which we develop and the language of that culture.

Yes, different brains from different people are wired differently. Yes, people speaking different languages probably have different patterns of wiring in their language centers. Yes, there is experimental data which confirms that sensual wiring regarding color recognition (that's the only one I know) is dependent on culture.

Is that enough to claim that our sensual mapping of the world is "greatly affected" by culture and language? As I see it, the answer is a clear and resounding NO. Maybe you know more than me. The only instances I know about where we know that culture and sense perception have an influence on each other, is the fact that different cultures draw the line between green and blue (and other colors) in different places, and in the realm of hearing and understanding language.

Beyond that it seems to me that culture and language are completely irrelevant for basic functions like sense perception.

So a practice that was effective a thousand years ago may not work the same way for the modern brain. I see this as why Buddhism manifested in so many different ways as it spread from one culture to another. The brains of each different culture and language are all a little bit different, with significant ramifications for the type of practice that is effective for each culture.

You do not have to invoke brains for that. Culture can fully account for all the cultural variation you encounter in the spread of Buddhism. Tibetan Buddhism looks the way it does, not because Tibetan brains are different, but because Bon was there, and because Northern Indian yogis influenced its development by bringing in a rich variety of breathing and energy practices. Zen looks the way it does not because Japanese brains are different, but because of strong Chinese influences, Shinto, and a wide variety of sociopolitical factors...

There is no need to invoke basic neurology, where culture on its own will do the trick. When you can have a look at history, and clearly see the causes and conditions that shape practices, there is no need to invoke the prefrontal cortex.

I do not believe our brains are the same as someone who practiced a thousand years ago, and what worked then may not have the same effect today.

I believe our brains are the same as someone who practiced a thousand years ago, and that what worked then has exactly the same effect today.

After all you say it yourself: "The part of our brain that names things is the cortex. This definition of nirvana suggested that it was possible to stop the activity of our cortex."

It's the cortex where all the (minor and unimportant) cultural differences lie. You say that it's when the cortex shuts off, that the important stuff happens. That's why the important stuff remains the same.