2004 Jeep Wrangler Rough idle on freeway, engine will die w

I have a 2004 Jeep Wrangler Rubicon, 6cyl. Automatic trans and no modifications to the jeep *yet. The mileage is at 31303.

Problem:
The Jeep, after approximately 30 minutes of running, will randomly develop a rough idle while in stop and go traffic or while driving on the freeway at any speed. The engine will begin to lightly shudder and it feels like the transmission is slipping slightly or wont shift up. The idle will shudder and if I come to a stop in traffic, or a light, it will occasionally die. The RPM indicator jumps up and down, between 200-ish to 1000-ish. I dont have exact numbers.

This began around 2 months ago and is random though it seems to be increasing in frequency. I drive 35 miles to work each way and it may shutter once each way. The check engine light comes on also, yet after sitting at work, it clears itself out and does not appear when I start the engine to leave work.