You should feel free to try anything you want. In data mining, it is not uncommon to try dozens of transformations of the same variable, and then select those that seem to work best. EM offers a series of "Best Power" transformations (Maximum Normality, Maximum Correlation with Target,...), and each one will try for you several transformations: x, log(x), sqrt(x), e^x, x^(1/4), x^2, x^4. There isn't a rule regarding whether to do transformation, selection or imputation in a specific order. Try different things, and see what works best. EM makes it so easy that I don't see a reason why you wouldn't want to try different approaches just for the sake of curiosity. G
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