1) For the sake of brevity LDR file uses the same submodel for both axles. You, however, need to put the 20-tooth gear on the other side of the 12-tooth gear on one of the axles!
2) There are several not-so-legal part placement, but it's okay. No excessive stress is incurred.
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These types of files are created with the LDraw system of software. You will need to install compatible software to open and view the instructions. A full list of available software is on the LDraw site.