Get yourself some squared plastic 'strips' from Evergreen and use them to line up sides at 90 degrees. Place the two parts together with a bit of glue then glue the strip in the corner to create the perfect right angle. Superglue when you have what you want.
For the crates, draw the parts onto plastic card, use a knife to score the plastic, then get a very coarse bit of sandpaper and use it to score the 'wood grain'. Then snap the parts out of the card. Use liquid poly. For joints, use Milliput or any other epoxy putty that you can clean up just after application before it dries. Then you won't have to sand the putty and remove the 'wood grain' lines.