So basically I am just theory crafting a few builds that I have used before, and I am going to calculate all of the damage each of her spells will do with each of the builds to figure out just ho much the difference in ap and magic pen really matter. I will be doing these calculations for various MR levels as well.

The formula that I am using to calculate damage is
Spell Damage = (Base damage+AP Ratio*AP)*(100/(100+((MR-MP)(1-%MP))))
Once Magic resistance is below zero the equation becomes
Spell Damage = (Base damage+AP Ratio*AP)*(1-((MR-MP)/100))
After Magic resistance becomes negative %MR penetration no longer takes effect.

This Data takes into account my rune page, but does not include stats from the masteries. I may change this soon.

These conclusion are invalid as of now. An error was pointed out to me. I am in he process of reevaluating.

After I have done the calculations I have determined that my 5th build is the best build against opponents who have magic resistance equal to or less that your magic pen. In this case this build is most effective until the opponent has 75 MR. This build consisted of a sorcerers boots, haunting guise, rabadons deathcap, abyssal sceptor, rylai's sceptor and Morello's evil tome.

At 75 Magic resistance my 2nd build becomes the best build. The difference is that in this build a void staff is substituted for the morello's evil tome. A similar result could be attained by removing the rylai's instead. The item you remove is just preference as the AP difference is 5.

At higher MR levels (represented by 200 in the calculations) of Magic resistance the 4th build becomes the most useful. In this build the haunting guise is exchanged for a void staff instead of the rylai's or morello's. The result is that the build has less flat MR penetration, but has more AP. The abyssal should be kept because it still grants a large damage increase against the champions under 50 MR.