So I want to give this run a crack and had a few questions. Is there a category that covers "All Missions, Both Episodes"? Or is that assumed to be under the "All Missions" category?

The closest category to that would be 25% which is both Episodes, All missions and the Soul Eater + Akiko's Frying Pan sub-quests. Basically it's normal mode 100%.

There are no Episode 2 quests at all in Offline mode, unless you have PSO+ (which are just a couple of pre-downloaded quests from Online) so there's no real need to include Episode 2 in an "All Missions" run.