They will deefinitely providing the 2 are the same model. In 2004 the Allison tranny was available in a 5 or a 6 speed. Before 2004 only the 5 speed was used. If one is changed for the other there will be shifting issues and codes set in both the ECM (engine control computer) and TCM (transmission control computer). Make sure you are putting in a 5 speed Allison tranny.
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