Kyle,
 
	 
 
	I had something similar that took me way too long to chase down.
 
	 
 
	My 99 Pathy would behave wonderfully when cold, then after about 30 mins, I would stop at a stoplight, in Drive, even with A/C on and the idle would fluctuate and then drop to 500ish and stay there, feeling like it was idling weirdly, like it wasn't smooth and it was going to die soon. I got a few check engine lights for Misfire in Multiple Cylinders, Running too Rich or too Lean, and after quite a while I got a Cat code. 
 
	 
 
	Finally, after replacing the MAF sensor and cleaning it multiple times, checking for evap system leaks, turning the distributor a bit to increase idle, cleaning the intake manifold multiple times, checking the IACV, messing with fuel pump and whatever other random things I could come up with I decided to check the O2 sensors. Unplugged the upstream ones and went on a drive. No change in the bad idle.
 
	 
 
	A few new O2 sensors later, no idle issues. 
 
	 
 
	I'm curious to know if you have the same issue.