CoD's GUI for controls isn't the most intuitive, but it does work well when setup properly- and it can utilize more controllers than IL2.
FFB is not something I use, so I will let others comment on this, but IIRC there is a 'trick' involving full movement of stick that cures this.
Setup:-
starting with the basics- you are assigning the axes properly?
http://www.justflight.com/supportfaq...liffs-of-dover
also when you have them assigned you are hitting APPLY? not hitting 'back' which will revert any changes you have made.
http://forum.1cpublishing.eu/showpos...31&postcount=3
might help re sensitivity etc.
Your CH controls- are they setup as a combined device through CH manager, or are they being seen as separate devices?
Also you mention using a CH throttle aswell as a quadrant- I suspect when you tried to assign the quadrant after assigning throttle you are going to have a conflict.
Throttle axis controls all throttles, throttle#1 only controls #1, if both are assigned confusion may result with the last signal overiding.
Use the CLEAR button to clear throttle axis if you wish to use quadrant.
I can also see a potential problem or 2 in your channel stop mission - ie you have used a mod ship then removed mods-This might be a problem
conf ini for mods is also kept in a separate location so changes made to one will not affect the other. In Documents/1C SoftClub folder there are 2 subfolders if you have applied the TF mod:
the original 'il-2 sturmovic cliffs of dover' which affects the original game, and one with '-MOD' suffix for TF version of the game.
(When you get setup with the original setup and you wish in the future to reapply TF mod the copy the ini files into the MOD folder.)
But that's running ahead, let's get controls working properly before looking at the other issues you are having