As part of my Mod I have five Spells with 101 Defined Effects, each one hooked up to a set of "GreaterThan" and "LessThan" Variables, so we'd have something like this :

Spell Effect 01 APPLIED IF Global01 IS LESS THAN Value01, AND Global02 IS GREATER THAN OR EQUAL TO Value02
Spell Effect 02 APPLIED IF Global01 IS LESS THAN Value03, AND Global02 IS GREATER THAN OR EQUAL TO Value04

And so on, and so on, and so on.

These are done on the Spell Record itself, not in a script, but the form where you define a Spell (Name, Cost, Effects)

Can anyone think of any easy way (even if it needs some scripting) of doing/automating this, so that I don't have to spend hours doing the same repetitive task again and again and again?

101 defined effects EACH? That's some crazy stuff you're doing there.

There are no automated task using the CK I'm afraid. Your best bet is using TESVEdit.