From experience I can speak that pen and paper are better for learning, but his system looks very exhausting. And there is a downside that his map of thoughts will not be encrypted.
I am an experienced programmer. I've been programming computers since I was 7 years old, typing in BASICA programs by hand on my mom's COMPAQ 8088. I formatted her hard drive by accidentally going into low level format instructions using ''debug'', experimenting with assembly language, when I was about 10. I am now 25. I love computers. I just happen to recognize the limitations of where we are at right now, that's all.
Computers will be the SALVATION of this whole system I am describing right now. So if you feel offended knowing that I am dumping on them right now, know that that's not going to be the case for long. Paper is unwieldy, large, requires storage, and a host of other ills. Copying from page to page to page is just a nightmare. It is a necessary nightmare, right now, but it is a nightmare. Computers will save us from it.
Hah! I'm sneaking in a #3. (Part of my ``no-edit policy'' when spitting stuff out. Apologies.) I WILL DESCRIBE, if I DO NOT FORGET, just WHAT steps you can take NOW, IF YOU ARE INTERESTED, to ``get the ball rolling''. There are some easy programs that you can make right now that would make this system AWESOME. I just don't have the time to code them up right now. But I will describe them, and if you like, you can code them up. Hell, I'll even throw in a description of the ideal computer notebook system- assuming I have ``magic paper''- and how it will dramatically increase our intelligence, provided that we can solve the versioning problem as well. (Note: Ted Nelson and Company went pretty batty WRT the versioning problem. Did they solve it? I don't know. I have heard rumors that some of Ted's protege's work for the CIA now, though.)"
Taking into account that you've written this when you were 16 years old (2003), this certainly means a lot to you and I don't want to interfere with anyones beliefs. I also do believe in computers so I can relate.
Edit: http://gtdtxt.tiddlyspot.com/ seems to be an implementation.