There is a script that comes pre-loaded with InDesign called SplitStory. All you have to do is put your cursor in one of the linked text boxes and run the script. It will disconnect the threading and make each text box into its own story
Which maybe isn't what you really want. Dave Saunders wrote a script called DivideStory that breaks the longer thread into tow separate threads at the frame you choose.
If you put text frames on the master page, but don't thread across the spread, you can have independent left and right story flows when you place text.
The script did the job. Not at first as it turned out the vbs script had a bug that it didn't remove the initial frames after having duplicated them. So the document turned ot to be twice the size with half of the frames not connected and the other half connected. I could have lived with removing them manually.
But before I started that I decided to try the java script version instead and voilá, it did the trick.
So now I have a document I can start working with. Still don't know if the automated page sorter will kick into action.
I won't mark this as an answer right now as there seems to be some more work I might run into and I would like any feedback possible. Will come back however as it surely helped me a lot.
I think your reply may be what puts it together.
"If you put text frames on the master page, but don't thread across the spread, you can have independent left and right story flows when you place text."
I just noticed there is a thread between the templates for left and right. Seems like double clicking on it removed the connection.
The two answers together solved my problem. I'm back in business again.
Thanks a whole lot. Unfortunately I could only mark one answer as correct although I needed both.