logging on multiple characters at once in different windows

Is it possible to have a plugin somehow open another window with a particular world file, and interact with that window (e.g, sending commands)?.

I currently have a plugin running that produces items that will time out after a while, so I'd like to programatically log in a storage character, hand off the items, and them log the storage character out.

Yes, look up the "world" functions in the help. You should be able to see if a second world file is open, if not open it, and then send commands to it.