Hey, I recently played through the campaigns of both games using a 360 controller and joy2key with great success.
The first FEAR game and expansions would see both joysticks and allow you to correctly map them. Even though one could map actions to buttons in game, I ended up using joy2key to map the buttons to keystrokes and leaving the settings in game at default, which seemed like the most portable way to do this. In addition, FEAR sees the triggers as axis, so using joy2key also allowed me to map them as button presses. The experience was in line with playing the game on a console... the only thing lost was the ability to lean and there is no aim assist. However I got though on normal without too much trouble.
FEAR 2 is a different beast... it doesn't see controllers at all, so you end up mapping WASD to the left stick and mouse movement to the right sick, which can take some trial and error. I settled on mouse moment +/- 10 in the direction pushed with an acceleration level of 3 and a deadzone on both sticks of 15%... that seemed to be a pretty close approximation to the console version of FEAR 2 without having to change any in-game options. Otherwise, I did the same thing as I did for the first FEAR game and mapped keystrokes to buttons.
I hope this is somewhat helpful. I went back and forth on getting FEAR 2 because I knew it didn't have controller support and I am in a similar position as you are, but I put in the time to get it working in joy2key because I really wanted to revisit it on PC because I always thought it looked super washed out on the 360. Good luck!