Don't you just hate when you have had a problem for days and you finally ask for help, you happen to figure it out? I guess it's cause at that point you abandoned your train of thought.
Anyways for anyone else trying to get the analog features working for farious SEGA games and rebind them for your flightstick or steering wheel I've made a little chart so you can add the rebinds manually
Find your games keybindings file, as example i'll use Afterburner II on the MegaDrive. which can be found at: "/opt/retropie/configs/megadrive/Genesis Plus GX/"
In my case with filename "After Burner II (USA, Europe).rmp"
Open it in notepad and adjust your keys, here is an example of the default buttons, with the A,B,X,Y buttons added, and the vertical throttle removed.
I've also made a little picture you can use as reference, you'll find that under the code, it has all the numbers you need to use.
That's all, have fun setting up your flightsticks and racewheels on a 16bit console.