I must say, I am surprised to see that there are still people playing this game. It is a superb game and I thought I was the only one that was left on Earth who still take this out and play it sometimes.
Anyway, you all have some very good points and here's my theory+a bit of research on the internet. And yes, this is my first post. I only registered to put my opinion on this
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With regard to the Practical Incarnation. I do believe that it is quite possible and not really time inconsistent. Remember the purpose of the crystal. It was created to separates TNO identities and imprison him. If you go to the dialog, it says that the Good Incarnation is the feeling at the back of TNO's skull warning him. So my theory is this. The Practical, Paranoid, and Good Incarnation has always been with TNO. When TNO touched the crystal, it separated out his three major identities. There's the Practical Incarnation (I believe this is the neutral one because he does what needs to be done, good or bad things), the Paranoid Incarnation (I think this is suppose to be evil because he killed so many people), and then there's the Good Incarnation who change his nature through regret. All three identities have been with TNO all the time. I like 3 person living inside you and each wanting to get out and take control. When those things happened, death of Deionarra, rescue of Morte and such, it was the Practical Incarnation taking control. This theory, of course, is based purely on my reasoning. But I think it's a pretty solid one.
Now the mystery of the Good Incarnation and the name part. I think maybe, just maybe, that TNO's name is really Adahn, even though there was another Adahn created when you said Adahn too many times. But we will never know, it's not possible. I did read something about the first incarnation joining the Blood War. Apparently, he did it because he wanted his village spared from the razing of Baatezu, by offering himself in service to the Baatezu, Fjull-Forked-Tongue. What exactly his crime was, I don't know. I don't think we could find out either. But I have a strong feeling that it has something to do with the Blood War.