Rough idle
I would try unplugging the MAF and seeing how it runs on cold start up. It will set a code but will then discard the MAF data and just use your VE and idle tables eliminating MAF issues entirely. Since you're tuned we don't know if they tuned your MAF or not but you did change the intake which changes the calibration of the stock values, it shouldn't be that large but airflow is complex and can get uneven. It could have already been damaged before you cleaned it or the cleaning itself may have damaged it so it's easier to just unplug and rule that out. It's easy and free and crosses out a potential issue.
You really need a scanner to check your TPS, IAT, and IAC values, if you don't have one your really just guessing and winging parts and fixes.


