I was successfully able to mod an Atari 5200, 4 port, original console. It was quite a challenge, but what I did discover is there are not many resources out there for modding the 5200. Below is a schematic of the circuit that worked for me:
For the mod I did, I went with composite out, but you can just as easily do S-Video out. This schematic is a mashup of http://www.gamesx.com/wiki/doku.php?id=av:5200_s-video_mod and http://atariage.com/forums/topic/193474-better-atari-5200-s-video-mod/
This version of the 5200 video out differs in one respect, I replaced the fixed 2K Ohm resistor on the Chroma line and replaced it with a 10K, 20 turn potentiometer. I found I was able to adjust this pot until noise was more or less eliminated from the composite video. It may not be needed with S-Video. Another adjustment is on the 5200 board. There is a large potentiometer in the lower right quadrant that is the color adjust. I loaded up Ballblazer and adjusted the colors to what I thought looked most accurate.
The connection points are as follows:
My next project is to reverse engineer the 5200 controller to allow for the use of modern potentiometer based control sticks.
Here is the analog stick: