Some vehicles will get so crusty in the upper intake that the secondary throttles will hang open or closed and set a code (those equipped with dual intake). I've yet to hear of a problem with the secondaries on a 1998+ 3.2/3.5L.
It looks awesome having that baby shinny clean, but I bet the engine cant tell the difference. As long as the EGR can flow, the dual runners can flop open and closed & the TB is clean, it's all good. I'd pull it apart and clean it only if I had to pull it for something major. Coolant leak, gasket replacement, etc..
Joel