@jplank Was that it?
Someone suggested I SSH into the retropie and go to bluetoothctl and then scan now. I did so and neither of the controllers showed up. I rebooted and tried again, same result. Then I tried one last time to load emulation station and pair the controllers - and it worked right away.
The thing is that I had about 15 tabs open with any youtube tutorial and help thread that I could find and I was trying anything I could find. For me, it wasn't that I changed setting X and then it suddenly started working. I "think" the last setting I changed was when mitu suggested changing the pairing mode. I changed it back to default and had to try a few more times to connect before it finally did. There might have been some resetting in there. All in all, I spent hours trying to get it to pair. I hope you manage to get yours fixed in less time. I hope that helps a bit. Good luck!