Does ISO affect AF performance?
No, they are not connected in any way.
Unless you're using the contrast-detection in Live View, instead of the phase detection of the AF sensor. Though in that case the camera is, I think, choosing an ISO that is sensitive enough for it to focus, and then changing back to your selected ISO when you depress the shutter release.
Will the Canon 70-200 f2.8 focus faster then the 70-200 f4 due to more available light?
Maybe.
When the light gets low enough most AF systems will start to struggle, a wider aperture gives you more leeway when it comes to low light AF performance. With adequate light, it probably isn't an issue.
Some cameras have certain AF sensors that are better at F2.8 or larger. For example, my 20D cameras have a centre AF sensor that is a cross type sensor when used with F2.8 lenses but only a linear sensor with slower lenses. That could certainly make a difference.
The actual speed of the AF is mostly a result of the camera's AF reading and processing abilities and the motor in the lens.
To expand on that, (it may look like I'm picking on Big Mike with these quotes; I'm not, just expanding) this is something true of all Canon cameras. Generally, at f/2.8, all of your AF points are working quite swimmingly. On the 7D, for example, this means that all 19 AF points are effectively cross-points. On the 1Ds MkIII, all fifty some odd points are at their highest sensitivity. But, on Canon cameras, once you start using slower and slower glass, those cross-points fall-off FAST, turning into less-accurate horizontal or vertical points. Around f/5.6, even on a 1Ds MkIII, only the centre point is still a cross-point. Same goes for the new 7D. Nikon cameras, on the other hand, have more sensitive AF systemsor so I'm toldand this fall-off of sensitivity at the outer cross points is less pronounced.
The overall effect of this is, that in any situation where fast, accurate AF is a necessity, on Canon cameras, f/2.8 or faster glass is the most preferable option, by far. Even at f/4 things fall off quickly. So the main difference between two lenses with different max apertures, when put on the same camera body, is not AF speed, but rather AF accuracy.