I think the Doctor used the Demat gun from the classic series in someway to remove the Daleks and Timelords from history (I think this is suggested in a comic). When used on one person, the gun causes memory loss, on a two whole species, well, it might just be fatal. I believe here Eight turned into Nine however I also saw something recently that made me think again, can't remember what though.
Also, I don't think Nine is newly regenerated in Rose, he seems to question his appearance but I think he is doing that in a general way as opposed to a first time. You can take it as a general sort of statement on himself as opposed to his first analysis thanks to the wording. This also helps explain his appearances in Clives images, the Who Is the Doctor? site, his ability to deliver a letter in that Peter Davison audio story, I think he also has an appearance in a spin-off book as an unnamed character and that first story with Sally Sparrow. This idea is also supported by the Tenth Doctor novel The Eyeless where they explicitly state that he travelled by himself first.
God, what was that thing? It really made me think again but now I can't remember it for the life of me.

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Also, Eight was planned to turn into Nine in a comic defeating the Cybermen (ironically dying the same way Nine would later; by Time Vortex absorption) but this was changed as I think the comic writers wanted to continue having Nine travel with the then current Eighth Doctor companions and the show writers didn't want this. Who knows what this implies about the Time War. It might suggest Nine fought it as opposed to Eight.
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