In researching CAIs and tuners, I've seen posts that you should reload the stock tune before taking your truck to the dealership for service visits. Can you run the 3.5" AF1 on the stock tune or do you need to reinstall the stock intake as well?

 

only the 3 inch ( maybe 3.25) can be run on stock tuning. Even then it may run WAY lean. So yes if you get the 3.5 AF1 you would need the stock intake.