In case you're looking for a "press this button and it will work" solution, this isn't it, but I can walk you through what you've tried and maybe help you sort it out that way if you like.
Here's an example with 16 text frames linked into one story. All 16 frames are on one page, which I realize isn't what you have, but it works for a visual.
1. Go to the beginning of the second chapter. In this case, I'll say it's frame 7.
2. Place the cursor before the first character of the text of chapter 2.
3. Select all of the text after the cursor by hitting the End button while holding Shift and Command.
4. Cut the text (you can paste it into a small frame on the pasteboard if it makes you feel safer. You won't keep that frame when you're done, so it's optional).
5. With the Selection tool, double-click the out port of the frame at the end of chapter one (Frame 6, in this case). That will keep frames 1-5 as one story, and 7-16 as a separate story.
6. Click into the first frame of chapter 2 with the Type tool (or double-click with the still-selected Selection tool to switch to the text tool and place the text cursor) and paste.
You now have all of chapter one in it's own threadded story, and chapters 2-end in a second. Repeat the process to make chapter 2 separate from 3-end, and so on.
I don't use the two scripts you tried, but I'm pretty sure that they will break each individual text frame into it's own story, which isn't what you want. Unless you find a better way, the method I have described will work, but maybe not as quickly as you would have hoped.
One last thing, each chapter will have a separator at the end, rather than the # symbol that indicates the end of a story. That's because we placed the cursor after the separator at the end of the chapter and instead selected the text from the beginning of the next before cutting. If you prefer to keep things tidy, you can delete those extra next paragraph/next frame/next column characters either with the story editor or with the Remove Trailing White Space GREP (just be careful to only apply it where needed, in case it messes up something you hadn't intended).
Dave Saunders wrote a scripte called DivideStory.jsx that automates splitting a story into two parts at the selected frame. He wrote it up at http://jsid.blogspot.com/2005/08/script-of-day-divide-story-into-two_31.html
The script was written for CS1 or CS2 and does not work directly in later versions, but it will work if you put it into a subfolder named "Version 4.0 Scripts" (without the quotes, and makes sure you spell everything correctly).
I was able to find a solution it was similar to what you both said but a little easier and also I found a script that is available on Adobe. Read this article.
The script was developed by Adi Ravid and is available at the Adobe Exchange. It allows splitting of all frames in a story, splitting before selected frame, or splitting after selected frame. I’ve used it in CS4 and CS5 (not yet in 5.5) and it has worked perfectly.
- Break the text thread between the frames by clicking the out-port of the last frame in the first story, then clicking that same frame. All the remaining text becomes overset, and the rest of the frames are now empty, ready to receive the new story.
- Edit the story in Story Editor (click in the text with the type tool, go to the Edit menu, choose “Edit in Story Editor”).
- You’ll see that all the overset text is clearly marked and easy to select in the Story Editor. Select and cut it. Close the Story Editor.
- Paste the text into the empty frames.
In essence, this is what the script is doing for you automatically. It breaks the thread, selects and cuts the overset text, and then pastes that text into the empty frames. If you need to do this often, then the script will save you time; however, if you plan your documents well, hopefully yo won’t need to do this often!