Wow what a mess we have going on here. Like other have said, if your OP holds true, then you are not tuned correctly and are going to cause irreversible damage and end up with catastrophic failure.
Cobb does support the aem intake on their maps which are available on your accessport via their website. However, I believe it's for the cold air intake, not the short ram. You would have to call cobb to find out for sure.
Here's what you need to do. Take off the aftermarket intake, put the stock one back on. Then flash the stage 1 map from the accessport to your car. (make sure its the correct one, for the right octane fuel you are using). Once your car is safe and properly tuned for, you need to read and research.... A LOT.
You cant just throw modifications and random tunes on these cars and hope for the best. Unless you have thousands of dollars to waste on motors and don't care about blowing them up and are just trying to experiment.
But do some homework, if anything we mentioned in our responses confuse you, then you are not ready to start modding your car or flashing different maps to your ecu.