Cobb offers a tune for their intake at S1/S2 power levels. I wouldn't install it until you have a way to deal with the MAF scaling.
You shouldn't need an intercooler at S1/S2 power levels. There is no base map offered by Cobb that will account for this. It could put you into untuned load cells, which could cause issues. You'd only know by datalogging.
You can get custom tunes instead of base maps like Cobb.