I don't really think the late-game damage is as big as you think though. Completed by itself, it offers 1000 Mana and 45 AD (+2% of whatever your Base mana is at a given level). For AD champions, at level 18, that can get around to about 65 total AD, sure, with no other Mana items, which makes it fairly gold efficient, sure, but there's still better options out there that DON'T make you wait until level 18 to get those kinds of stats.
On top of that, you're talking about a passive on Transformation to Muramana that usually takes until at least Minute 15-20 at the earliest? Even saying you have another Pickaxe to get at the same fold value of your opponent who built I.E., that's likely only about 80 AD you have and 1500 mana. That's only a 10AD advantage, really.
So now, every AA or single-Target spell can deal an extra Average 60 damage? Nice, but that won't continue to scale much past that, as opposed to the Crit builders who WILL continue to scale with more Crit, and more AD.
MF I can see things working with her abilities a bit, because she does have the Lethality build direction, but I don't think it adds enough. Also, if this WAS so effective, then Trinity Force would probably add more for her if her Base AD scaling wasn't one of the worst in the game (for good reason mind you, considering her kit). I'd honestly prefer to throw another 500-700 gold into building Ghostblade or Duskblade over manamune instead.
But really, fixing the item is what we should be thinking about, and the transformed passive should be what makes this worth buying, and that's where I feel the item is kind of confused.
Mana is a stat based on wanting to do sustained damage, but the passive doing damage based on CURRENT Mana is kind of contradictory to that, as the longer you sustain damage, the less damage you do. I think consuming 3% of max mana to deal bonus damage is great for it, but we need to figure out how that damage should be calculated. Right now, its identity is a little confused for that. Or hell, let the bonus damage on here crit, and make a build with E.R. Would actually be kind of interesting. Turn Muramana into a replacement for I.E.