You are diving into the deep end. I imagine that controling an aircraft with this sort of precision is an extremely big challenge. But, regarding your question;
First, I am not certain you understand how the Sharp distance sensors work. They emit a beam of IR light that is seen as a dot on the object being measured (well, you would see it if you could see IR). Then, a lens focuses the image of that dot onto a linear sensor (sort of like a camera, but with only one dimension, not two). How far left or right that focused dot falls on the sensor is what determines the distance.
Other, cheaper, IR sensors work by simply emitting an IR light (fairly broadly) and then a sensor simply detects any reflected IR light. The brighter the reflected IR light, the closer it is presumed to be. So, it doesn't really detect distance. Rather, it is detecting if something is close.
Neither of the above are good methods for distance measurements if you are tracking a small point.
Ultrasonic range finding is another option, by perhaps having the drogue emit a pulse of light and an ultrasonic "ping" at the same time. Your airplane would then look for the light, and listen for the ping and measure the time difference between the two to determine the distance. But, I suspect that there will be too much noise in the environment for this to work.
This leaves using two cameras to see your infrared beacon on the drogue. The difference in the postion on the image on the two cameras is the method of determining distance. It would also tell you the direction of the drogue in relation to the airplane. The CMUcam has the ability to automatically track colored objects, and communitate the coordinates to your CPU over a serial connection. Perhaps simply provding a red surface on the drogue is enough to target it.
Joe Dunfee