To be honest, I think you have a good understanding. Some of my hangups were similar. The way that I have been moving on is "well, if that's the way it is, then that's the way it is". Just accept the idiosyncrasies and plow forward. PHP does some of the same things (variables can show up out of nowhere, etc...). Just code the way you want to code and if it works, then great!
Then after you get to that point start breaking out the profiler and see if there's anything that you can optimize.
Here are a couple of things:
If you understand CSS, then jQuery selectors should be easy. As far as the code goes, that's straightforward too if you can deal with chaining and JSON. EDIT: also, the jQuery documentation on everything is EXCELLENT! And There is no shortage of jQuery experts here on SO to help us noobs (and hopefully we can return the favor for newer noobs).
There is a scope to work with. (Basically) anything written outside of a function or object is in global scope. If you are inside of an object or function and use then that sets the variable's scope
The #1 thing that threw me for a loop is that any JS that appears anywhere on the page or that was included in tags is fair game. If you have a global variable in one script, you can use that same variable in a completely different script and it will work. That may be what you mean about variables showing up out of nowhere. Also, there are some DOM based variables that can just "show up" too.
Anyways, I think that if you just plow ahead, you'll get some "AHA" moments. I'm a relative noob to programming, but I continually grow as long as I don't hang up on something that doesn't have too much of an impact on actually making the code run.
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