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I would suggest going with an Arduino Nano rather then the Boarduino. I looked into the specs for the Boarduino and it uses a Ceramic Resonator rather then a Crystal for it's reference clock. With the ceramic resonator for timing the base accuracy is less and there will be greater fluctuations in accuracy with temperature. Since you probably already have the Boarduion you might want to look into the possibility of switching it to a 20Mhz crystal for better timing accuracy and resolution.
Mike
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