cp-e has a velocity stack in the filter for their 3.25" and not an actual air straightener like shown....as long as there's something smoothing the air in front of the MAF.
as for the 3" intake, follow what Fobio posted above with regards to AccessTUNER. your MAF g/s values need calibration and you might want to start by increasing the lower part first since your car won't even start and idle.