If it worked before you put the cold air intake on and doesn't after, the problem is with the installation, not the computer. It should run fine if the only thing you changed was the intake tube and air filter.
Did you reconnect the smaller tube that runs out of it? Also double check your MAF connection and make sure thats secure and I would recommend disconnecting your battery for a few minutes and let the ecu reset, that will take away the dash lights.
MAF is likely in the wrong position, or no longer clean enough to pick up the sensor properly. ( I had this issue on a short ram intake, I moved the MAF closer the throttle body by 1 inch ) fixed my problem.