I believe you would have to get the tunes adjusted. Adding a CAI or Gotts mod can make a difference in the performance. The best way to take advantage of one is to have a tune telling the truck what to do with the extra air. Since your tunes were for the stock intake, you would probably have to get your tunes adjusted. I'm not sure what all has to be changed, but I think the Air to Fuel ratio has to be corrected.
I just bought an AEM intake and I'll be installing it next week. I don't have custom tunes yet, but I'm about to buy them. I know the canned tunes were written for a stock intake, which provides less air flow. By adding the CAI, it increases the amount of air the engine gets, and the fuel amount stays the same, causing a leaner condition. I would think it would be same for a custom tune written for a stock intake.
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