I did a similar project to this and I would love to know more details on what you did. I took the PCB of the controller, unsoldered the triggers and joysticks and then I connected digital potentiometers to replace them. It worked flawlessly with controlled input.
That being said, my buttons were nightmares. I used an exacto knife to scrape the trace and solder to that tiny tiny piece with enameled wire. It was terrible and unstable. How are you handling your connection to the buttons?
I was helping another forum member in this post with the same thing you want. He wants a macro ability to take panorama shots in halo reach. He said for his buttons he used fine grit sand paper to remove the coating on the button pads which gives him a much bigger solder joint. I did enameled wire and hot glue, which is similar to yours.
I removed the sticks and triggers from mine, I just want the board, so with that being said, I would love to find a version of a controller that has ample test points for buttons and sticks. I'll look into the Matrix model you described and see. I'm using a wireless CG model.
In the above post, it shows where to order the digital potentiometers for free (University or work email), and how I used them so give it a read and feel free to ask questions!