Hi ya Moltke, well I dont have the MS FF2, but I will say that CH pro pedals should work with any stick. They are a separate usb device so as long as the game you are playing is able to use more than one controller at  time. CFS3 does, as do most all modern sims, only some older games such as Falcon 4.0 do not.
However, CH controllers come with a nice little thing called "control manager 2.0" which can actually combine two or more controllers into one device so as to be used in older games like Falcon4, however I believe it can only do this with CH stuff.

I myself have three CH controllers hooked up, the pro throttle, pro pedals, & combatstick.
All three are USB, and all three are working in CFS3 just dandy, and I didnt even have to use the control manager at all as the controller set up utility in CFS3 worked quite well for assigning/re-assigning axis's & buttons. 8)

Heh, I might also recomend CH products to you as they are the best on the market other than the Thrusmaster HOTAS Cougar, but I havent been able to find the Cougar in any of the stores at all, and besides the price for the combatstick & pro throttle together was about the same( I allready had the pedals, as well as a CH yoke.)

So yeah, get them pedals, you will love them, and wonder how you ever got along without them!
BTW the CH sticks have built-in mechanical trim wheels for both X & Y axis a real big plus! More than worth the $99 - $129 they cost.