Also just bought a 2000 TJ, 4.0L inline 6, 5 speed tranny with 36,000 miles. Ran fine for a few days, then I let it sit for about a week. Had some heavy rain during that period also.
Anyway I got in it today and could not shift into gear. Tried with the motor running and off with same results. Then I remember how I would sometimes have to rock my old MGB years ago to get into gear. Tried it and it slipped right into gear and away I drove. Only thing I've noticed that could indicate a problem before this happened was 1st gear seems a little sticky, as in kind of jerky, even when I feather the clutch.
Any ideas? What does rocking the thing do exactly? And does it indicate a serious problem, or is it just a jeep thing?