Ioryogi's war with heaven was certainly not explained... in fact this anime has an 'original ending' since the manga has yet to finish. Sadly I can't find scans about it... but I head rumors of them visiting other planes.

Though the manga doesn't have many of the crossovers this anime had, save for Chobits. I think adding Wish to the anime was excellent.

Which brings me to the next point... there was already a war dated on Wish, though we didn't see it either, so I guess its not rare for having one here as well.

And I think you and Shinta hit the nail. That Kiyokazu from the dream was most likely another incarnation of him.

I guess it wouldn't have any impact on the characters... but I wonder if returning them their memories of Kobato affected somehow. I mean... they didn't remember her for who knows how many years and then she suddenly reappers on their minds?