As for the whole Ear,l Mana thing, i think is indeed possible the earl had lived in his current state as if he was to be killed and reborn/resurrected/whatever, as if he was i would think it would be the memories of Adam, the Noah whose genes he possess that gets transferred not the ones of his old host or previous body (but seeing as no one has resurrected skin bolic yet, and i haven't yet read the manga though i have goggled some info, it is just speculation as pretty much everything else i am saying as once again i have yet to read the manga), Nea walker of course is at the moment considered a different case as he hasn't been defined as carrying genes of any previous noah (i.e the suppose original 12, the Earl carrying Adams genes, and being considered the 1st making the total 13).
Anyway back to the point so it is possible that the Mana is considered to have taken over was indeed a ancestor or just simple a different Mana, seeing it has been said only the one with the license can control the ark and the Earl was so hurt/mad about Nea's betrayal, and since the Earl knows how to control the ark (or maybe he just knew how to control the new one he build as he is the one who built it), but if indeed the Earl did know how to control the ark on considering it has been said that he seems to care for the 14th despite the 14th's betrayal could it not be that the earl thought the 14th how to control the ark and gave the license for the ark to the 14th thous making him the player, and therefore felt gravely betrayed when the 14th gave the license away to a human (though that human later turns out to be the one the 14th intends to make his host).
Again i haven't read the mana yet, i am downloading them as i write this and will see what i come up with after reaching the latest chapters, these are just my two scents from what i have scene others mention.