Dont overlook a vacuum leak, it could be an intermittent leak somewere that opens and closes... i've seen it
i second that.
take a look at the thermal vacum switch valves. they get old and break sometimes. and maybe after the motor warms up one of the valve opens and leaks.
also check out your egr components.
another thing to try is tounscrew the idle circut silinoid and remove the "O" ring from the tip, (save that "O" ring!), then screw the silinoid back in. this will bypass the shut-off circut.
the purpose of that part is to prevent diesiling when you shut the motor off. so if you run with it bypassed it is good to run you idle a little lower than normal.