OK so the difficulty thing I got working fine so that now hides the arrow and action presses.
I've ditched the idea of going directly into the Daphne Emulator at bootup since I found a better theme that I don't mind it as much having the option up there before going to the game selection.
So the only two problems I'd still like to figure out is:
Why in Dragon's Lair 2: Time Warp when I die it starts to play the death scene and then a second or two of another death scene before going back to the next life.
And the Cthulhu PCB not being recognized after it's reboot. Checked other forums regarding the Cthulhu PCB and no one seems to have any info with it regarding RetroPie and why it doesn't get recognized on bootup until it's unplugged and plugged back in.