So here's the gist of it - I have a "system" that won't start until the missing piece is replaced - player finds the missing piece, finds the empty spot, and puts it back... what's where I'm stuck.

What I'd like is for the player to be able to "click" (like an activator) in the empty spot and choose to replace the missing piece, but can I do that?

Other ideas are good too. I thought maybe a button or something, but that doesn't make sense insofar as placing something goes. Also, there are no meshes near enough to the empty spot to use as activators without it being obvious that it's the object and not the empty space the player is activating...

You can set the texture of an activator to the NULLTexture set. Simply click on the model button and in the field to the right right click and select add >NULLTexture set. You can use setdestroyed, or disable to toggle whether the player can click it or not.