Unity,
I was in a similar situation as you, but got the DS4 successfully paired today! My last install was only 1 week old, so not sure where it went wrong, but today I performed a fresh install and got it going!

My steps for successful DS4 pairing:

• Flash retropie 4.0.2.
• Sudo apt-get update
• sudo apt-get upgrade
• retropie setup script, update all installed packages (repetitive?)
• From GUI, Bluetooth pair DS4(#2) using wired DS4(#1). (No freezing while "searching" this time!)
• Configure input GUI, hold down a button on the bluetooth'd DS4(#2) and configure inputs
• Shutdown system
• Unplug wired DS4
• Power up
• Turn on DS4(#2), sync'd right up as player 1, hotkeys and all input working

It must have been a config file issue that was preventing the sync before, because I had performed all of the upgrades on my prior SD card, but this time around it worked wondefully! I have not attempted to sync 2 DS4s at the same time, yet.

P.S. I did zero of the 'extra setup' shown on the github for DS4 controllers. The native packages work for me now. I hope this helps you!

Good luck!

I'm really pretty embarrassed right now, but it was because I only had my wireless keyboard plugged in and not any gamepads. Hooked my snes controller in and it booted right up. Thanks for your help and I hope this will help others who have this problem.

@mikeyb Hmm...how did you transfer the games over? Did you enable samba shares and do it that way? Are each system's games in /home/pi/RetroPie/roms/ ?

Cause yeah the systems should show up in emulationstation as soon as there are rom files in those folders.