Ok, so for the Free Edge part, I just created a Setting Adjustment and put a "1" on the Maximum Edges field to give the 1 free edge. It is presumed the player will use it for AB: Super Powers but the book allows for it to be used elsewhere, so it's just a free Edge that can be used however the player likes.
I don't see that I have anything for Super Karma, though.. hmm...
The only other things I have put in it were 2 Ranged Weapons (Hvy. Sniper Rifle and the M2-Herokiller), the Setting Adjustment mentioned above, ammuntion for 3 types of Herokiller bullets and Teflon Arrows, 3 types of armor (Modified Fin Combat Armor, Personal Combat Armor and the Z-Belt), a Mechanic to set starting cash to $1,000, 4 special weapons, the Mechanical Genius Edge, 3 pieces of Equipment, 9 Vehicles, 3 Races (for Atlanteans and the hybrids) and 1 Racial Ability (Telepathy). I believe everything else is covered in the SPC.
Super Karma is supposed to be handled on the Character Configuration screen under the "Super Powers Companion Settings" there is a subset of "Genre Conventions" and "Super Karma" should be selected there. That should cover it. But if that doesn't work you should probably post a bug report here about it so one of the Lone Wolf folk can address that.