BruceO, I'm absolutely overwhelmed!
Your research certainly traces the tune at least, over many miles and to many places. Thank you for all your work. It's always amazing to me that folk music seems to just incorporate change of time and location, without losing anything of the spirit behind it.
The more I've thought about it, with regard to Parnell, the more sense the lyrics make. The verse with the questionable line, for instance, talks about a sort of "whistle stop" campaign that Parnell had been on, just prior to coming back to Avondale. But before he had been home for even a day, I think, he was called to Dublin, and en route, he was taken prisoner and put in Kilmainham. The song is from the viewpoint of Katherine O'Shea as the personification of Ireland. In Irish myth, the country has always had a feminine personna, and she's both warrior and mother.