Ok.....so, you replaced the OEM Cold Air Intake with an aftermarket cold air intake. Now, you have trouble.
Just a thought.....perhaps the aftermarket parts are causing the trouble.
FWIW, I installed a K&N system on my long past 6.0L GMC...... I thought it would add 1-2 mpg....in truth, it did nothing. No power increase, no mpg increase. Although, it did lighten my wallet and increase throttle sound.
Then I got curious to look beyond the marketing hype. Reality, the reason those "flow more air" is because the filtration is lower. In other words, it will allow bigger dirt particles to enter the engine. The "power gain" doesn't happen until the engine is pushing redline. Not many daily drivers push to redline. Also, the "market numbers" are from a specific test engine on a dynamometer, which may not be the engine in your truck. These CAI were developed for racing applications. These race engines are frequently disassembled and repaired after each race. Not many daily drivers disassemble their engines each week.
Suggest to remove your K&N, then reinstall the OEM system. Your troubles will likely go with the K&N.