That's a nice box! I think increasing the first stage reduction a tad would be a good idea to get your high gear below 18fps, below 17fps, really. I've packaged that reduction before while maintaining good tooth contact.
You also need to move your CIMs up so that the belt doesn't touch the middle pulley twice, as it appears to do now.
How is this 3lbs without CIMs!? It should be 2lbs max from what I'm seeing here.
Are you using aluminum pulleys?
EDIT: Oh, are you using Vex pulleys? Switching to 3mm GT2 pulleys from SDP-SI will probably net you better results and let you mess with the ratios a bit; you may even be able to get them from faster sources. Of course, figuring that out before build season would be necessary. Given the design you have right now, it might be easier to switch to a 3 CIM gearbox than lower the speed.
On the extending the output:
I already spoke to Chak about this, but I think you can just press out the roll pin. What makes you hesitant to remove it? It seems like something people do fairly often in other applications.
EDIT: If you make a length of thunderhex and retain it some way other than using a roll pin in the ballshifter output socket, then you don't need to worry about high tolerances or roll pins. A shaft collar between the gearbox and 2x1 should suffice.