CGR

So I have a 2007 SCT Tuned Mustang GT, and I was having hesitation and idle problems due to my spark plugs needing to be replaced, but I'm doing that tomorrow afternoon.
I installed a Roush Cold Air Intake it had a rough idle, so I replaced my beyond filthy worm MAF Sensor, and still was having idle problems, just not as bad. My wrench light that bad been on since I installed the intake, had turned off and everything was fine and I drove it around the block, aside from the hesitation from plugs, it started and went right up to normal idle, then right when i pulled back into my driveway the wrench light came back on.
Does anyone know why this is happening? I got my engine light scanned from O Reilly's, and Autozone, and the paper said it was recommended that I replace the throttle body, and I know these have bad throttle body issues and I already have a GT500 upgraded throttle body coming in, so that might be it, but I'm not sure. Any thoughts?
Some people told me I should just get retuned, so that could fix any problems, but I'm not sure.