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I'm not completely sure that you could replace a 9V motor with a power functions one. The issue is 9V motors and battery boxes were often structural to the model. Now that's not to say that you couldn't rebuild the set incorporating a power functions motor, but that's not really the same thing as a substitution.
However it is the barcode reader that is essential to this set, I do not own it, but I understand from reviews that it is a bit of a weak link in the set.
The barcode reading aspects of the set are interesting but not that impressive and once you've played with them a couple of times you'd be bored of them, so don't sweat if it doesn't work.