I have weapon racks that did work fine. But now I have the entire setup starting disabled, and becoming enabled through a quest later, all at once.

The problems:
-any weapons linked to the displays just sit where they are in the CK instead of snapping into place on the display as they should (they are all linked from the correct places)
-I can place as many weapons as I want on each display as opposed to just one per display
-once I place the weapons, they can't be picked up again in most cases

-this includes full size and dagger cases
-this also includes the vertical weapon racks, though I can pick up weapons on these
-this includes single weapon plaques, which I can at times pick up at odd angles from the plaque

Is the enable/disable process responsible for this?

For the first problem, yes. The second and third problem seem related. Did you use an enable parent, for both the triggers and activators?

Yes I did. I'm curious how Beth solved this...

If it worked until you had disabled them, perhaps just set their scales to 0 initially, then to 1 when the time is right.

It's been a while since I took a look at the scripts for the weapon racks, but I remember that there was some code in there that enabled/disabled the trigger from the activator, depending on whether or not there's an item in there.

Since you're using an activate parent for the trigger, it might be overriding the enable/disable commands from the script, which is causing the weapon rack to malfunction.

Anyway, you can take a look at how the vanilla player homes dealt with this, or just follow JustinOther's suggestion.

Yes, I think you're right. I removed the enable parent on the orange half, and when the blue half spawned everything worked fine. So this leaves the issue where the activators are always there... so I may just do the scaling idea.