Is there anyway to change the actor effects of a creature through a script? I want to remove one and add another.

I'm not sure if theres a way to do it via script. But could you perhaps have two creatures, each with one effect that you want, then just swap them out for one another?

Yeah I had a similar thought, but I wouldn't know how to do it. I want to change the actor effect, or swap the creature when the player uses an activator. It would be affecting the base, not any one reference.
Also, I'm having trouble finding good documentation for the base game script commands, If you know of good place to find that, I may be able to work something out on my own.

You can use the WIKI.
http://geck.gamesas.com/index.php/Category:Functions

That's what I've been using. I think I found a way to do what I need, i just changed the effect script to check a variable and either do its default or my addition based on that, however i cant get the activator script to modify that variable.
I tried using an example I found in sticky's scripts... "set StickyRef.goodbyeStage to 1" But I cant get it to recognize the variable. It is "set effectIDRef.variableName to 1" correct?

Well it depends, where did you place the variable? Its the ref of the object the script is running on that contains the variable that you need to put. Also make the object running the script with said variable a persistant reference.

Currently the Variable is on the effect script and I am trying to change it via the activator's script. Should I have the variable on the activator script? If so, how do i check that variable from the effect script?

I got it working now, turns out i wasn't using the reference correctly. I moved the variable to the activator and got it to check that variable from the effect script.