Is there a solution to this yet? I had the same experience on phone from level 2 and from a repair call. Bought the printer brand new a few days ago.
Please PM me the log number associated with your/your IT dept's call(s) to Xerox when you/they spoke to 2nd level support.
If you can't print to tray 5, and tray 5 isn't actually broken (Works as a copier) then they would have escalated the issue to 2nd level support (Not an onsite tech).
Somewhere in your job it is requesting portrait 8.5*11, you need to find it to resolve the issue, the Document Size (Apple) and the paper size (Xerox Features > Paper / Output) or somewhere in the Application itself.
MS Word is the problem, it is over riding the driver and specifying for 8.5*11 instead of the custom size (I'm assuming you did set the size and tray in the Xerox driver here).
Shown below is the way I've loaded the paper and the job status messages and job details. I set up in the control panel the dimensions, paper weight, and color (I just chose green because that seemed the closest color to scantron, although white paper color didn't make any difference.)
Got a screenshot of the error on the device? If it is asking for what is currently in the tray, it is almost always because of Stock type/color being wrong, or the wrong orientation, and the little warning screen actual shows which way it wants the page loaded.