hesitation issues


for those who have done the air box mods we all know the low rpm hesitation it produces. then magically around 4K it disappears and things run super smooth. well last night the hesitation didn't go away. I reved up to 7K and it finally smoothed out a bit. my question is what changes at 4K to make it smooth out. and what would happen that it would no longer change like that. is there a sensor somewhere going or gone. I did some searches and the IAT looks like the most probable piece to look at but I just wanted some confirmation of that or if someone else had this same issue and what they did to fix it. I have my stock 01 ecu I could put back in but will that work with an 05 rotor on the stator ?