Originally Posted by Infinite

The airbox and snorkels shouldn't require a retune. Make sure the maf is tightened down and is pointed the right way in the intake. If the maf was dropped or shaken hard it could have gone bad. They have a crystal in them that is very sensitive to shock loads and g-forces.

Unless the check engine light on the dash is on, there are no codes to check. If it is on however, most local auto parts stores will pull the codes for free.

I'd put the stock airbox back on and see if the problem still presents itself. If the mb box somehow came off the rubbers slightly that could cAuse the rough running due to a post maf air leak.