Filing the USB connector hole at an angle towards the top of the box on the inside will help here - just connect up the pigtail connector, coil the wires at the bottom of the box as best you can (a better job than I did here would be nice!) and slide the dongle in while bending the heatshrink on the pigtail. Try and make the connector at a right angle as well - the configuration shown below is putting a little more strain on the dongle's antenna connector than necessary.
As you can see here, I elected to keep the SMA connector in place with epoxy resin. A nut and washer would have done the job a little more neatly if I was able to source them.