xterra2k, I got the mirror from xterraparts.com. It is actually the passenger side vanity mirror from the SE. If you look at yours you will see two screws that go up into the roof. It unscrews and the other fits perfectly (no difference whatsoever) into the same area.
My guess about the holes is food and water with a hole to re-fill them. Too low to actually do without folding the seat, but if they put it higher it would not work for most dogs. While the holes might be strange, the cage is actually much better quality than I expected (for $150)...
Sean