Well the RTE has nothing to do with scripting and probably actively makes it worse/more frustrating, so you're good on that front (I've never used it because it seemed clunky to me).
Now, don't get me %this or $that because I have no clue what you're telling me when you say that. If I did I could probably have figured this out by now.
Yeah, this is
the start to understanding scripting. Once you understand the variables, like 99% of those articles you were stuck on will start making sense.
There are three kinds of variables: user variables, system variables, and constants. Each type of variable has a different prefix sign, which you will need to use every time you reference a certain variable of its type. For example, you can't use the system variable sign $ to refer to a user variable % because CYS will think the variable doesn't exist. So you can't say %PAGEID unless you literally created a variable named %PAGEID, and you can't say $AMMO to access your variable named AMMO that you created (you'll have to use %AMMO).
User variables are the variables that you created for your story (including the default SCORE). These variables are marked with a percent sign "%" to show that they are user variables. User variables can only contain integer values (so whole numbers, positive or negative). The most common use for user variables are storing character stats. Think values like %STRENGTH, %HEALTH, %MONEY, %AMMO, %ENERGY. At the more advanced levels, you can use user variables to create combat scenarios, store relationship statuses between characters, and more.
System variables are variables that cannot be created by you. They are part of the scripting system, hence the name; their values can, however, be modified. These variables are marked with a dollar sign "$" to show that they are system variables. $PAGETEXT is a system variable, and it holds all of the text on a given page. Some other system variables are $PAGEID, $ITEMSTATEX (if X [where X is the ID of an item in your story] is or is not in your inventory), $ITEMUSEDX (how many times X [where X is the ID of an item in your story] has been used), and $DEST (determines what page a reader gets sent to).
There are also constant variables, denoted by an at sign "@". These are variables that cannot be changed. They are regularly used to specify page/chapter IDs (ex: @P39 is page ID 39, @C3 is chapter ID 3) and innate destinations like @SAVE (the save game page), @END (the end game page), etc. because these IDs cannot be changed. You can change the name of a chapter or a page, but not its ID. $DEST uses constant values to determine where to send a reader.
TL;DR: user variables is stuff you make, start with %, only integers. system variables is stuff made/tracked by the system, start with $, value can be changed. constants is stuff whose value cannot change, start with @, usually used for direction via $DEST.
So now that that's squared away, hopefully that makes the articles seem less intimidating.
With that being said, my recommended reading for each question:
1.
How to Create a Great Title Page - obviously a specific use case but the fundamental concepts are still there and can be applied via HTML/CSS
2.
How to use Random Variables - read this first to understand how the dice system in CYS Script works and how to read the dice notation, then read
Scripting Random Encounters and Events to see some examples on how to apply the random variables practically via $DEST handling
3. Since you're familiar with Java, just think of if statements. That's basically how you handle PAGETEXT changes depending on variable, just with different syntax.
How to Use Scripting to Improve your Story has multiple examples on exactly how to accomplish this in CYS Script.
Oh I had a bunch of stuff on HTML too but I didn't want to give you a bigger wall of text than I already wrote because I'm horrifically bad at explaining things an appropriate amount. Check out
W3schools for a super intuitive HTML/CSS resource.
