I'm terrible when it comes to numbers lol.
I'm playing as a Breton Mage.
Bretons come with a 25% magic resistance right?
With the blessing of Mara it adds 15%
- Totalling 40%?

If I were to enchant some gear to fill in the last 60%, the take the apprentice stone (100% weakness to magic).. Would magic then do 'normal' damage to me?

No, magic resistance is capped at 85, so you would still be 15% weak... I think. It depends if the Apprentice stone's affect applies before or after your magic resistance.

Personally, IMHO, the Apprentice Stone is about the worst stone to pick for this game. Weakness to Magic is not worth the increase in regen rate. Particularly when there are enchanted items and magic regen potions so easily made that help this. What I miss is the Mage effect from earlier games. Anyway, the Atronach Stone might be better for a mage in this game.

Also, this. For a mage, I'd pick the Atronach, or one of the general stones like the steed or the lord.