CAUSEDODGEPATTERNBALDNESS
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The 5.2 supposedly actually has slightly more timing than the 5.9 PCMs, so in theory it could actually be better. The biggest difference is in the O2 sensor and cat layouts. R/Ts are all over the place depending on year as to how many they have versus the lower level trucks. A '98 4x4 5.2 Dakota, for example, has two O2 sensors, in pre and one post cat. The '98 R/T has 4 sensors, but only the one cat. Later trucks can have 4 sensors and 3 cats if they've got California emissions. In theory, a '99 Federal Emissions 5.2L PCM in a '99 Dakota R/T should be fine as it wouldn't care about the two extra sensors, but you couldn't do it the other way around since the R/T PCM would be missing the two O2 inputs.