Exactly what I did. The Toyota air box is actually not a bad design. Get rid of the resonator, remove the foam baffling, and get an AFE high flow filter. I added a Verus shield and a Forge separator. Looks great. I honestly think the Toyota air box is flowing as much as an intake, but don't have...
Been in automotive design and manufacturing for 20+ years. Besides, they confirmed to Lordhowe they did a fit up on their test car after he contacted them. So yes, I know enough.;)
If they have a good QC program they will do a first article and in process inspection during a run. Eibach makes good quality stuff in the automotive space, I would bet they do this.
You can put in a higher flowing drop in. Couple good ones out there. It will improve air flow. In general though, CAI don’t give you huge gains anyway.
A good PDR guy probably can get the panel straight, but paint, always a touchy subject, Might be a good time to replace the vented panel with CF. Insurance for sure.