Are all your other screws in and tight? Loosen the crap out of them, and try to move the board so that you can get that last screw in. I've used boards ok with as little as 3-4 screws in so ONE missing shouldn't be a problem.
So I built a new pc and tried to align it with the io shield but no matter what the pin sticks out for the ethernet and one usb port so i took them off.
Huh? Pin sticks out? Are you talking about the I/O shield?