In regards to Fandaniel's madness, assuming that it's a legitimate desire to destroy everything, it could simply have come about as an evolution of his character over time. He may share the Ascians' belief that mortals are inferior beings, barely qualifying as life, and ALSO have come to the conclusion that the remaining Ascians, both Sundered and not have become so depraved and corrupt that they, too, are no longer deserving of salvation.

It doesn't have to be something he inherited from the original Fandaniel. He may simply have changed over twelve thousand years (or however long it's been since he was raised to be an Ascian). He's accepted that the Ancients' time is done. Their world is dead and gone. But that doesn't mean he's going to hand everything over to the worms that infest their world's corpse now - no, the best way to memorialize the past is with a world-sized tomestone...

I also tend to think that the memory stones did not so much "rewrite" the memories of the raised Ascians so much as it JOGGED them. Whoever Fandaniel was before he was raised up is still there, but he also has access to the memories contained within his soul fragment. In the case of most Ascians, this is enough to get them to side with the Ascians' goals - but in Fandaniel's case, he merely decided to play along (or, perhaps, was legitimately on board at first, but changed his mind later).