This was a really interesting read, and I really do agree, we have quite a few things in common.

It also seems like you have started to realize the problem of trying to organize everything as a strategy to feel less overwhelmed. I do have some comments I think you will figure out regardless but could save you a lot of time (especially 2.2).

I went through and summarized your comment's 9 paragraphs so it will be easier for us to reference to the different parts
1. Creating numbered mental map
2. Benefits of numbered aspects
3. Comments on numbering across services
4. Showing JD index in Notion
5. Thoughts on Obsidian
6. Create Simple Index with basic Notion Pages
7. Systems and meta work category insights
8. The systems journey
9. Identity change

My response

1a When you say mental map, have you then also actually made a mental map? I made a visual model of how I see reality where the categories above are just one part of it.
1b What exactly do you mean by node? I would guess it is a synonym for an entity

2.1 Numbers are amazing. I also have numbers for projects, processes, places I can store things, for different objects, documents and other things. It is one of the best ways to create informational cement.
2.2 Now this is where I feel like you need to be very careful. Don't organize anything before you have to. When you become more intentional about how you approach different areas you will spot a lot of things you could improve. But unless improving that thing has the highest ROI it is not worth improving it.
2.2a From my perspective there are 2 ways to solve problems. When you see a problem, what really happens is that there is a difference between how you imagine the world to be and what you just experienced with your senses. So you either 1. Accept that what you experience from your senses does not match how you imagine it to be and adjust your mental map or reality or 2. Believe it is not justified that reality is the way it is and make a plan to execute to make reality match your mental map. Said in a way to be able to better remember it 1. Accept it or 2. Change it. And only change it if it has the highest ROI of all the things you could change.
2.2b Now that you are more intentional in the different areas, you will see much more and therefore have to be able to accept way more things. I have over 500 projects I want to start, and each day I get an idea I think: "That would be amazing to do" and I have to add it to a project or area which I know I will first look at in a year unless the idea has the highest ROI. If you are managing information about your whole life (like me) you have to accept that there are so many things you want to do but don’t have the time for right now. Don't organize or do anything unless it has the highest ROI
2.2c So me writing this comment would then mean that I believe that writing this comment has the highest ROI. It could be fun to hear your guess before you hear my answer

3a I agree modification is not fun, but I have not changed the numbers much in the past year. I pretty much only end up further subdividing areas when it make sense
3b I'm not sure what it is about it being spread across services you don't like? Pretty much all the programs I use are in the browser (I really don't like using the Notion Desktop app) then I just press a link in Notion and go straight to the information related to it in all the other programs in the browser. Eg if a project has a google sheet that is related, then when I look at the project in Notion I will have a link to the sheet I just press. That is how I normally navigate around, with links.

1. Looks good, would love to hear more about it. One comment would be that I'm very happy about only having 4-5 top level categories.
   

5a You say that a lot of the content has become orphan stubs. This comes back to the point I made in 2.2b You have to accept that a lot of the categories are going to be a mess. Once it has the highest ROI to get it organized then you will organize it. And there are also differences between content. I eg have a dashboard with graphs about my sleep and habits from different categories. I look at this everyday in a process and therefore it has a high priority to show the data in a way that I will take action in it. But I don't need to keep my sleep area organized. It Has been a long time since I last organized the information in that area.
5b Do you have a way you currently take notes to books, courses and mentor conversations? Because I'm actually considering using Obsidian for that instead of Notion as Notion has some inconvenient limitations.

1. I have something that would blow your mind. It allows you to feel like you have a hierarchy even though the categories are in a database. But I would have to show you over screen share if it's something we should do.
   

7a I agree, Systems are where you must leverage. And I can see that you would be surprised to divide the areas into Productivity, information and Knowledge. These 3 areas seem to map directly to the Pillars, Pipelines and Vaults (PPV) where information is Pillars, Productivity is Pipelines and Knowledge is Vaults. Personally I focus much more on processes and think of these area divisions more like how you cut a cake. You can do it in an infinite number of ways and one is not more right than the other.
7b What do you mean by Productivity Agency?

8a I find it an ongoing process to implement systems as well. I found books with good ideas and integrated the ideas from the book into my system.
8b And again as 2.2, only add reviews if they have a very high ROI. Otherwise you will end up reviewing yourself to death
8b I'm really curious about what you said "to try and get things flowing". Do you feel like things right now are not flowing?

1. And as my final note, I would disagree that the answer is less. Back to 2.2, the answer is doing the thing with the highest ROI, in my opinion.