So the Key to this setup is the MaxShooter One. It allows control of the PS4 via keyboard commands, the thing is you have to leave a PS4 controller permanently connected to the MaxShooter for this to work. The Flirc is connected into the MaxShooter in the same place a Keyboard is usually connected. Its a bit of a crazy setup but it works. You can map L1, L2 etc. and all of the buttons on a PS4 to a Keyboard (the FLIRC).
This setup worked 99.9% of the time with the exception of the FLIRC sending random commands to the MaxShooter once in a while. These random commands would interrupt any movie/game being played on the PS4. Really annoying and I never was able to get it fixed.