To the first point, we don't actually see Franklin and Sheridan meet in Season 2... and they wouldn't be apt to talk about a secret mission. But Franklin would, of course, like a peace mission -- so when he says that he's liked what he's seen of Sheridan, that actually computes. Yeah, it's mostly a retcon, but whaddya gonna do?
Delenn and Sheridan being captured is covered in the Centauri Prime trilogy of books. That's actually not a retcon, since JMS knew how it was going to play out, wrote it into both War Without End and In the Beginning, and finally handed the story off to the books' author to finally set down on paper.
EDIT: I'd have to get up real early in the morning to beat Jan to an explanation...