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I've uploaded some schematic drawing. There are actually two types of 28BYJ-48 motors. They are almost identical, except the mounting holes: http://thingiverse-production-new.s3.amazonaws.com/renders/6d/99/73/f6/cf/28BYJ-48_preview_featured.jpg
In blue is the more common motor with only two mounting holes, in black yours with four mounting holes. I can adjust the models so you can mount both types, but it will take me some time, and as I don't have them home, I am not sure about the result. Sorry for inconvenience.
Or you can drill two more holes in the position mentioned in blue. They don't have to be 4.2mm dia. 3mm would be enough. There would be just very little metal around the hole, but it should suffice. You will also have to put some washers under mounting holes of Z and Y motors.