I have an 01 TJ with the 4.0L 5 speed. I was going to work this morning, about a 10 mile drive. It was cold this morning, about 30 degrees. I let her warm up idling in the driveway for about 10 minutes before departing. I took off and got about a mile from home when she started slightly shuttering while in gear. When you took her out of gear, she would roll just fine, no noise. But while in gear it felt like there was extra drag on the motor and I could hear a faint clunking noise coming from underneath me.
The check engine light also popped. I'll have to pull out a scanner tonight and see what it's complaining about.