The Dureena/sword story has certainly been mentioned, but I'm not sure it ever got to the script stage. That would have been a mni-arc extending over several episodes. The episode where she actually gets the sword was not among those published on-line at Bookface.com. I think she may have had the sword in one of the Bookface scripts, though, since I believe one of them took place after she got the weapon. (It was written earlier, though, because it was slotted earlier in the production schedule.)
The two scripts dealing with the Shadowtech/EarthGov plot were not intended to air back to back. "To the Ends of the Earth" was slated to shoot as episode 114 (production order) and would have aired fairly close to the mid-point of the season. JMS's idea was to air the minimum number possible of the early "black uniform episodes" - say 4 or 5 - then "Appearances", then the grey uniform eps - then "To the Ends of the Earth" (which contains the famous laundry accident that sends the crew "back" to the black uniforms.) So it would have aired somewhere around episode #12, maybe #13, or S1. "The End of the Line" (production order 116) was the S1 cliff-hanger, and would have aired as episode #22 - 9 or 10 episodes after "To the Ends of the Earth". "Value Judgments", Fiona Avery's Bester script and the third script published at Bookface.com, would have shot as episode 115, in between the two JMS scripts, but I'm not sure when exactly it would have aired (other than that it would be in the second half of the season.)
Regards,
Joe