Narfellus,
i think we can port most of the system without much problem, for instance i don't see why we should worry about Certmén, since I don't think the proposal is to have magic traditions be so widespread and respectful as to accept that kind of duel, concentration is the easiest element of those, since it creates the lesser of all troubles, magic theory is the best match for Knowledge Arcana or maybe spellcraft, or maybe both, no big deal, parma magic is a trick one, my first reaction was to make it a skill then I realized that if we want magic to be a part of the game and not controlling it we have to accept the idea of spells allowing saves most of the time.
Then Parma magic could be made into another technique, then you would cast a parma corpus to try and create a repulsion like effect on all humanoids around you, this is what I think might chime in easiest.
Penetration is too deep in the Ars system in my opinion, casting speed could be taken care differently, no fast cast spells, for example, but you could always ready an action and since you will get a save, that perdo corpus spell is not that terrible, after all, it would not allow one otherwise.
What i think we have to think about is lab, longevity potions and D&D magical items, this needs some working to make both into a coherent whole.
As for Wizard's Twilight, i have not read much of it but I guess it can be implemented, with the right thoughts and concerns, in midnight it could be attached to the astiraxes and their ability to find magic emanations, for example.
You should really try a kind of Ars d20 without telling your players, start them as commoners and let thing sgo slowly, much like starting a Mage: The Ascencion game before the awakening.