I agree in general with not having a class but instead making him a special case or his own class. He basically invented a class and allowed several classes to exist, so it makes sense he'd be outside the limits of classes. But to try a class...

A refluffed Ur-Priest to make it non-evil?
Cleric X/Ur-Priest X/Wizard or Mystic Theurge X, handwaving the requirements of having arcane casting beforehand.

I like Vogie's idea of thinking the God of Knowledge was holding back. Perhaps through experimentation or finding secret knowledge, Arkis figured out a way to sap into the god's power without permission. Through this, he not only regained some divine magic that was otherwise now lost, but also drew forth the knowledge of arcane magic.

I somewhat recommend Ur-Priest because that gives him an unexpected ace in the hole, namely some divine spells when folk would expect him to only have arcane spells. Could be useful as a surprise, if you want such for your campaign.

Alternatively, Cleric X (with lost spellcasting), then Wizard to denote how he figured it out. Not as exciting, but it makes sense. He figured out basic magic and became a wizard, then kept figuring it out until he was a level X wizard.

If you want to surprise players more, use Paladin instead of Cleric to give him martial weapon proficiency. Still lost abilities. Maybe he was LG, but upon realizing the limits his god was putting on mankind, considered the god a hypocrite and drifted to TN as he sought knowledge over what was handed to him by his deity.