Looks like this is going to work, except that viewing about 50% of the different upgrades causes my editor to crash.
EDIT: So I'm going to create all my upgrades from scratch. Since each hero will have 4 abilities, I am going to make 4 abilities named "Ability 1" etc. and then make 4 copies of each upgrade i make ("Stun 1", "Stun 2", "Stun 3", "Stun 4").
EDIT: Also, when I use an ability that has more than one effect, only the first effect goes off.
Last and final EDIT: I created a persistent Effect, then clumped all of the other effects I wanted in to that persistent effect. Then, I created requirements and validators that I will have users "research" through my triggered dialog window, essentially adding the effect to their custom ability. After that, there will be upgrades that decrease cooldowns, increase range, etc. Figuring this all out took 7 hours. Phew.