Didn't have any problems when I transitioned, but that may be my mind is younger then you old farts and can get use to it quickly.
While it's not realistic, one thing I've noticed helped was reversing the pedals. By this I mean the Right pedal turns you Left and vice versa. Seems more natural for me, so I don't have to stop and think about which one to hit. Think it may be I'm use to hitting Left and seeing a Right reaction and such, as with Racing games, watching a car at the starting line, pressing the gas pedal (right pedal) makes the car tilt to the Left, the Brake/Reverse (Left pedal) tilts it to the Right. It applies to other things, take a box for example: Press the Left back corner with your hand and it turns the front to the Right.
Just something to try anyways. The option for reversing them is: Clipboard>Options>Map Controllers>Highlight Rudder Axis>Advanced>Check "Reverse Axis".
That was the big thing for me--for decades playing in the snow..skiing, steering sled, etc...I always pushed my right foot to go left, and that was my instinct when I got my CH pedals,so I inverted them. Helped tremendously. Alas, if I pick up my flying lessons again, it could be dangerous.
I'm thinking of switching the inputs back to normal, and suffering thru a month or 2 of even stupider deaths than normal, until it seems normal. Of course...THEN I could break my neck skiing or sledding....sigh