This gets easier with practice. You need to make sure that your spring guide is seated within the grooves that keep it from moving around. I like to start from there when bringing down the one side of the shell and then kind of pulling the tab on the spring guide towards the front of the shell so that I can shut the top part around the cylinder head.
At that point, you should be close to aligning the shafts of your gears to the holes in your bushings. Press down hard, then grab a 2-3mm flathead screw driver, and press on the shafts to guide them through the bushing holes. Same thing with the ARL. Everything will just snap into place.
Another tip is to weigh down the trigger with the end of a heavy hammer or other tool so that it doesn't pop out or fly around.
Once your mechbox is closed, take your long 2mm hex driver and stick it in the air seal nozzle to push your piston. Make sure the piston can move up and down. Check the springs on your trigger, selector plate, and press the nozzle in and out as well. Those checks will alert you to any problems that have crept up.
Now you know