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The only anomaly I saw on my 6.0 when I did it was I need to cycle the key twice to start it. If I cycled the key once to start the gages won’t work and it will not turn over. Cycle it again and it is all good.
Are there any issues/ill effects regarding the PCM when the batteries are disconnected for 2-3 months or even longer?
You do realize old PCM's on shelves and in junkyards being used as replacements are just bolted in and hooked up without anything being done to them first, right? There would be no difference (ill effect wise) compared to your PCM unhooked for 2 or 3 months.