We also implemented a dual cylinder pneumatic launcher - similar to what you are trying to achieve. There are a few things I would do to yours to maximize your launch:
1- At the back of your launcher arm you need small "armlets" (we called them) that will cradle and hold the ball. This will be the last point of contact as the ball is going through the arc of the launcher and will (drastically) effect the launch trajectory. Your launch appears to be going more up, and needs more forward. The angle and length makes a big difference - even a 1/4 inch changed distances and heights for us.
I had a proto launch video that I cant find , but I will link these two of our completed robot:
http://www.wicz.com/news/video.asp?v...Eflv&zone=News
http://www.wbng.com/news/local/Tiger...249661331.html
You can see the geometry better than I can describe.
2 - You are giving up a good amount of energy by only using half of the stroke on those pistons. You can pull them backward or raise them up and use up more stroke. I don't think you need a third. Based on that, you need to be mindful of cam-locking the throwing arm.
3 - I agree with the gate latch and pre-pressurize the cylinders in a retracted position and then just release the latch. (It worked for us).
Looking at your construction - You will need to heavily reinforce it. I know it's a prototype- even what we did in our competition robot was put under immense stress and pulled itself apart and needed reinforcement during the regionals.
Airflow was a bit of an issue as well and we minimized all runs of tubing and extra T's and such in the system.