Ok, well heres the rundown. It was stalling like a month ago with a CEL and it was a o2 sensor code. I also had a bad cat. So what I did was bought a new o2 sensor on it and gutted the cat and of couse put a mil eliminator on that o2. Well, it started running good, no stalling for 4 days, doing great. Well last night I got a CEL and had it checked, it was P0172 and P0411, and of course the P0411 was that hose unhooked, and I plugged it back in. With that CEL on it still wasnt dying. I hooked the hose back in and unhooked the batter for 10mins and started it and let it idle for 3 fan engagments. No cel still, drove it around for test drive to make sure everything was cool and it is now it is dying sometimes at idle like it used to, sometimes it will just dip low then catch itself. Its weird becasue it seemed like with the hose unhooked it wasnt dying and now with the hose hooked back in it is. wtf is the deal? Do i need another Mil eliminator on the other o2 possible or what? Awhile back i did the MAP whack, and I also cleaned out the TB.

 

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If you are expieriencing the idle dips, don't try and correct or compensate with throttle. Let the idle "freak out" on it's own. If you have just reset the ECU it takes time for it to learn how to idle correctly. Even if you have performed the "idle learn procedure", which it looks like you attempted. It will take a while for the ECU to "learn" how adjust everything for your ambient conditions and achieve a smooth idle.
Does your car idle fine if you leave it sitting at idle? Do you expierience the "dip/stumble" when you press in the clutch and are coasting to a stop? If the car "dip/stumbles" when you are coasting to a stop does it occur just as you reach 0mph?
If you answer yes to all 3 questions, I think you are most likely just expieriencing something normal related to the ECU learning.
It can take a little while for the ECU to smooth the idle out. I personally think it takes a little longer if the ambient conditions change alot where you are (temp, bar, etc change often and drastically). Also it is important not to try and correct or compensate with the throttle while the engine RPM is stumbling, let it fall on it's face if it wants to.
It may also be worth noting that an S2000 can stumble occasionally even after it has "learned" to smooth the idle. It should never be as pronounced as after it has recently be reset though. To me it seems like a heat wave can induce this behavior to some extent. Under these circumstances it usually only seems to affect the car in the first 15 min or so of driving.
Also the engine Idle learn procedure is not a count of how many times the fan comes on. It does sound like you probably completed the procedure if your fan cam on 3 times. What you want to do is start the car and warm it up with all accessories and HVAC off (fan come on and goes off). At this point begin timing 5 min. At any time during this 5 min period that the fan comes on, do not count this time toward completeing the 5 min. Hope that makes sense and good luck
EDIT: also to reset the ECU in MY01 pull the no.25 7.5amp "backup" fuse from the cabin fusebox/panel for 60 sec. No need do disconnect the battery.

 

cool, yeh it idles fine, drove it today and it seemed like it was doing perfect, I apprectate it....went down just the way its suppose to, hopefully it wont do it again...but after today, I dont think it will