It could be one, both, or none. Has it been recurring or just a 1 time event? Have you tried disconnecting the battery for about 10 minutes to allow the computer to refresh with the new tune and intake? I have always disconnected the battery to clear the computer after installing anything aftermarket. Is your canned tune compatible with your intake? I would start by calling the tune maker and ask the question about compatibility with your chosen intake.
Others on here know way more than I do about this truck, so hopefully they chime in.
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