The guide you have followed is pretty dated now (although it seems updated in some areas).

I would be tempted to use either 2.6 or 3 beta 4, both found in the downloads area and write that image. Can you try this?

– Download RetroPie 3 beta 4
https://www.petrockblock.com/retropie/retropie-downloads/retropie-project-sd-card-image-for-raspberry-pi-2-beta/

– Extract the image and write it to your MicroSD with Win32DiskImager
– Boot up the Pi, which will configure your controller.
– Quit Emulation Station and expand the filesystem (sudo raspi-config)
– Write your rom file across and try again?