I might dig up the force feedback code and put it in CVS for whoever wants to try it but it's going to be a build option and an ini option. Oh and you'll pretty much be on you own if the code causes your FF joystick to go insane and attack you.
Mod directories are off of ~/.fs2_open/ and off of the main directory where you have the game installed (ie, it checks in $(HOME) first and then the gamedir). The "-mod" cmdline option allows you to specify one or more directory names to use for mods. I use "-mod scp,mediavp" when I'm playing a normal game. Then I have two directories, ~/.fs2_open/scp, and ~/.fs2_open/mediavp that the files come out of. Anything that gets saved (except for logs and pilot files) will go into the first listed mod directory. I tend to use different game directories for total conversions like TBP, WCS, and Inferno but you still have to specific a -mod directory to keep all of the files separated in ~/.fs2_open. The only restriction on what the -mod directory is is that it has to be lowercase, no exceptions.
You can also go deep with it, "-mod mods/scp,mods/mediavp", if you wanted to keep even more order in your directories. There is a path length limit (consider max length of 128 though it's larger in some areas) for the whole thing so try not to bury the files too deep or it won't be able to find everything.