I use a 20D,many times with the 100-400L IS. I never noticed any change in AF speed wether I shoot Raw or JPEG. In fact, the choice between these two image filing procedures should only affect the speed of recording on your camera buffer (internal memory) before transferring it to your CF card. That is why, when you shoot in burst mode, the number of consecutive images your buffer can accept is less in Raw(heavier files) than in JPEG(lighter files), and you can't shoot while your camera is busy to transfer from the buffer to the CF card.
The autofocus speed is independant and should not be affected by the filing system you choose.
J'espère que c'est clair, sinon je vous l'explique en français plus tard.