Yeah that DC jack pin is generally called the "spring" from what I've seen and it isn't used. I think I wired them both up to ground because I can never remember which pin is ground so having them both be ground is a no-brainer. It will be fine without that pin.
I also printed out several 1:1 copies from eagle to test sizes and measurements. It is definitely helpful. Are you concerned about a via on the back of the LCD shorting from the USB shield? You could always just put one of those felt feeties on the USB jack to insulate it. The annular ring around the LCD screw holes are also electrically isolated I believe so it won't make a difference if they touch.
I'd be happy to look it over, even if something would have to stick out pretty badly for me to see it as being wrong. Just zip up the brd/sch and email it to
bmayland@leoninedev.com when you're ready.