Yeah, they need to check out what is causing the issue. A WOT tune isn't going to work well on a street driven tune when compared to a live tune. I'd still say put a new MAF on there and get a live tune. I would toss the MAF and get a speed density tune if it were me. I'm loving mine.
Oh yeah, you still need the IAT sensor so you cant toss the MAF unless you install a Camaro type IAT sensor to do that duty.