I called Pioneer to make sure the files were right. According to them, even though the name is saying AVIC5000NEX, it's the correct FW. I'm not exactly sure why they can't use a better, less confusing name, but the Pioneer rep I spoke with even told me to refer to this instruction guide which also says the oddly named file is the correct one.
http://www.pioneerelectronics.com/StaticFiles/PUSA/Car_Electronics/Firmware%20Update%20Files/NEX%20&%20SPH%20iDataLink%20Maestro%20v1.09%20&%20v1.10/Maestro%20FW%20Update%20Instructions%204000NEX.pdf
I installed it on my unit which is now