I don't have MergeTextFrames so can't tell if you are doing something wrong. I have an ExtendScript that I use (not extensively tested); but you could try it. It looks for all stories in the document (except those on Master Pages) and links text frames for the stories. The one caveat to the script is that stories have been added to the document in consecutive order. If you would like to try the script, email me at email@example.com.