I don't know of any good resources for learning what the forest is like. As far as I can tell, everyone who knows what the forest is like learned by learning about more and more trees.
Assuming your AP computer science class used Java, a good next step is to learn Python (probably using some resource like Dive into Python written for people who already know how to program) and learn the command line (using the Hard Way book on the topic or http://code.google.com/edu/tools101/linux/basics.html or something).
Then you can take a shot at following the instructions in the rest of this comment.
Using cron:
http://lesswrong.com/lw/2dg/applying_behavioral_psychology_on_myself/267c
Note that it assumes you're on Linux. I don't know the best way to duplicate my results on Windows.
If you're on Ubuntu, a good next step is to type "man gnome-terminal" from the command line and figure out how to use flags to cause gnome terminal to run an arbitrary program when it starts. Then you can substitute the command you construct for the Firefox command in the original cron example.
With lots of Google searches and persistence and trial and error, it should be possible to set things up so that you get a window popping up every hour with a random item from your to do list. You can complicate things from there as you desire. For example, figure out how to input some number of minutes that the window should wait before popping up again. There's tons of stuff you could try out.
Persistence example: if you get gnome terminal to start running a command, the terminal will close as soon as the command terminates. So you'll need to ask the user for input in the last line of your script. (In user experience terms, this will translate into you pressing enter to close the terminal window that pops up.) This is one of those things that could take an hour or so to figure out.
In general, you want to start by getting extremely simple examples to work and gradually modify them, making sure they still work after each modification.
You should probably ignore the JSON bit for now and craft your own log file formats; it will be more educational.
Feel free to respond to this comment with more questions. I'm counting on you to figure out a lot of stuff for yourself here. You're going to have to do this anyway if you're going to be a coder; you'll need a decently high tolerance for frustration. But I can help you out some in the early stages.
Presumably you read Less Wrong because you're interested in thinking better.
If so, you might be interested in another opportunity to improve the quality of your thinking: learn to code.
Like nothing else, coding forces you to identify flaws in your thinking. If your thinking is flawed, your program won't work, except by accident. There's no other discipline quite like this. If you're a mathematician or physicist and you solve a problem wrong, your paper won't tell you. Computer programmers have to measure their thinking against the gold standard of correctness constantly. The process of uncovering and fixing flaws in a program, usually called "debugging", typically takes up the majority of the time spent on software projects.
But this is only the beginning. You've probably heard something like "there are some problems that humans are good at and some problems that computers are good at". This is true. And once you learn to code, you'll be able to exploit computers to solve the problems they are good at. Having a computer to write software with is like having a hi-tech mental exoskeleton that lets your mind run harder and jump higher. Want to know what the second most common letter for an English word to end in is? That's a 15 line script. Tired of balancing chemical equations for your homework? Automate it.
Two more benefits that have less to do with thinking better:
Having enough coding knowledge to be dangerous may take persistence. If you tried and failed in the past, you probably either got stuck and gave up because there was no one to help you, or you just didn't keep at it.
I've take two different introductory programming classes now to meet college requirements. The students in both seemed substantially less intelligent to me than Less Wrong users, and most were successful in learning to program. So based on the fact that you are reading this, I am pretty darn sure you have the necessary level of mental ability.
Starting Out
I recommend trying one of these interactive tutorials right now to get a quick feel for what programming is like.
After you do that, here are some freely available materials for studying programming:
Here's a discussion on Less Wrong about what the best programming language to start with is.
If you're having a hard time getting something up and running, that's a system administration challenge, not a programming one. Everyone hates system administration I think, except maybe system administrators. Keep calm, put your error message into Google, get help on a relevant IRC channel, etc.
Once you've got the basics, a good way to proceed is to decide on something you want to write and try to write it. If you don't know how to get started, start making Google searches. Soon you'll figure out the sort of libraries/frameworks people use to write your kind of program.
At first you may just be aping what others do. For example, if you want to learn something called "bleh", searching on Google for "bleh tutorial" is a great way to start. Finding a working program and modifying it to see out how it changes is another good option. Soon you'll graduate to appropriating sample code from documentation. As you write more code and see more of the software landscape, you'll be better prepared to craft original approaches to writing software.
See also: On the Fence? Major in CS, Teach Yourself Programming in 10 Years, Computer Science and Programming: Links and Resources.