Stereo vision and object detection.

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In response to your questions:

1. If you want to do any sort of geometric reasoning about your scene, then autofocus is absolutely taboo. Auto focus changes the intrinsic camera parameters and thus makes estimating high quality metric scene geometry near impossible, and definitely not real time. The typical workflow with stereo cameras is that they are manually focused and rigidly aligned specifically for the type of scene, calibrated and then unchanged.
2. Autofocus may not have any effect on object recognition depending on your detector type. If it uses only 2d image information, then this will likely have little effect, but if the detector requires 3d information then autofocus will prevent reliable detection.
3. There are special stereo cameras like the Bumblebee you can purchase.

Since it seems you are very unfamiliar with stereo vision processing, I recommend read the chapter on stereo vision in Szeliski. You also should more clear on your requirements, are you primarily interested in doing object detection, or 3d reconstruction using stereo cameras? Both of these are active research topics, and they are only partially related to each other, i.e. you can do object detection without using stereo reconstruction.

EDIT: I forgot to mention one important aspect when implementing stereo vision. Most (all that I am aware of) stereo reconstruction algorithms make the assumption that both of the images were taken at exactly the same time, that the scene did not change. If your scene is not static (people or objects are moving in it), this requires that you use synchronized cameras (like the Bumblebee). USB Webcams are rarely able to be reliably sychronized for a variety reasons.

If you're going down the two webcam path and want to do simple parallel forward facing stereo, then I highly recommend you build a solid physical rig for it. The slightest pixel misalignment will mess up any 1D block matching algorithm.

Back in undergrad I was using two Logitech ball shaped webcams. I made two wooden pieces with holes for the camera to sit in, then used screws to clamp the wood together. Here's a poor ascii art:

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 /--\       |       /--\
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I was using some rather thin MDF wood and over time it would deformed. In hindsight, I should have went with much thicker wood.

Calibrating the two cameras was tedious and done by eye balling. Getting the vertical alignment wasn't so bad because you can see the two images side by side and make a good guess. To make sure the cameras were close to parallel I would focus at a very far object and made sure they're at about the same (x,y) position.