Seems to be working but when I set them all to zero, there is a small flash at what I think is midnight.
Try setting the sun texture and sunglare texture to empty textures, switching the day sky texture out for a darker one, and/or setting all the weather types to not at all bright and sunny.  That should at least reduce how noticeable that split second is.
How can I use an NPC's reference to modify the base value of their health? For example, the player goes into a cell, in it is an unknown NPC. A ref walk returns that NPC's ref as a reference variable. Using that ref variable, what function can I use to change the base value of the NPC's health. I do not want to heal or kill them, but rather for their "health" stat that you'd set in the CS. I hope that's clear. :/
http://cs.elderscrolls.com/constwiki/index.php/SetActorValue
 Sorry for huge post. Thanks in advance.
It would be nice if you would keep the title of the thread in mind when posting.
There is no need to have an empty GameMode block; it is superfluous.  The script will compile with only variables.
All variables start at 0, so it could be a bad idea to have "elseif (DrTrPortalQuestHolder.origin == 0)" for any reason.  According to your scripts, the only time it will ever be 0 is if the player has never activated one of your teleporters.
Because your activator scripts have onActivate blocks without specifying "begin onActivate player", it is possible that NPCs are activating the objects, which would set the variables in conditions you do not intend.  That seems unlikely, but it is possible.
Otherwise, I have no idea what is wrong with your scripts, because you didn't say what they are doing instead of what they are meant to do.  I don't see any other glaring errors, and the ones I pointed out are of little consequence or probability as your culprit.