When my car is at an idle my RPMs don't stay in one place all the time. It drops below and rises above 1000RPM occasionally. While I'm not sure when this problem started, and may not even be related to this next issue, I believe I started noticing it after I noticed the hesitation. If I'm in a higher gear at a lower speed and give it anything but full to the floor throttle it will hesitate while accelerating. Kind of like a jerk every second or so. I'm not sure how else to explain it.
Anyway, I first started noticing both of these after I replaced my air intake. I went to AutoZone and they pulled my codes, resulting in two running lean codes. I told them about my intake and they said the reason it's hesitating until I hit full throttle is because I have too much air coming in and when I stomp it it dumps more fuel into the mixture which is why it evens out when I do so. I'm wondering whether these two things are related and what can be done about them. The rough idle could be one of too many things, but the explanation I got for the hesitation seems pretty air tight(!).
(I've been told to put my stock intake back on and see if the problem persists, and I've thought hard about doing it, but it took me a good hour to rig my intake together (I've got my MAF sensor pretty snug in there with silicone all around it) and I'd hate to have to do it again..)