98 Protege rough or no idle?

Hey Guys.
I have a 98 Protege', 1.5L, auto, a/c..

Recently, my car has developed at idle issue. When I first start the car in the morning, it runs just fine. Idles perfectly. But once the car has warmed up, it starts acting up.
Once warmed, the car will either have a really rough idle or it won't idle at all.
I checked around under the hood for basic stuff like loose or bad vacuum hoses and unplugged sensors. All is well.
Checked the air hose from the MAF sensor to the throttle body. Its in great shape. No holes or cracks and still very flexible.
I did notice one thing that does have me concerned though. I hear a slight popping sound coming from the filter box coming down the line of course from the intake. Don't know if this would give any clue to what the issue is.
The check engine light has been on for over a year. I had it scanned numerous times and each time, the scanner says no codes to be found. Tried with several different scanners. Same thing. I disconnect the battery negative cable and turn on the headlight switch for a few min. Reconnect and the light is gone till I run the car for about 50 miles then it comes on again. Still no codes..

Anyone have any idea what to do with this?
Thanks

It really weird that the CEL light comes on with no codes .... I would hunt that down with the dealer to see how (if) that is even possible ... just to avoid chasing your tail.
I was having trouble with idle (it wouldn't) after the car was hot and sat for an hour or so. I traced it down to a sticky Idle Control Actuator. Try this next time it is acting up...Take a small hammer or anything that will yield a gentle tap, and give the IAC a tap (it is located on the top of the throttle body). If the idle problem stops the instant you wack it... you've found it.
The manual says to check the EGR valve for sticking, and also the EVAP solenoid to make sure it is not sticking open...

But honestly, since it is throwing a CEL that means that the ECU is not happy about something.... so you need to get to the bottom of that...

Good Luck

Thanks zogy..
It seems I may have found the issue with the no code thing. I broke down and went to the dealer. They couldn't link in either. They suggested a wiring problem or a faulty computer. The guy attempted a reflash, but could not get a good link. Sooo, they want a nice fortune for a replacement computer. I'll be scouting a couple junk yards for one just in case. The guy said he would attempt a reflash once I get myself a salvage computer. I'll worry about the idle once that part is taken care of.