Is there any way to make a lightning bolt do variable damage?

Could you use the fake lightning bolt and in the script section of the effect calculate the Health damage. I can't find any tutorials about putting a script event in that section and then making it run.

Since I have perk entry points on my mind...

You can give the player a perk to accomplish this.

Use the perk entry point Mod Spell Magnitude and condition it to affect only your specific spell. Perk Entry Points have a handy option called Add Range To Value that lets you add a random number to the value, which you could use to randomize the spell's damage.

Why use up scripting resources for that. You can make a spell with 5 or 10 low level shock effects at 10 different levels and each one has a random number condition.

Sometimes you will get 3 that work, sometimes 5 sometimes 2 or even none. If you do not want zero damage remove the random number conditions from one of them.