2002 Jeep Wrangler Intermittant misfire

My Jeep Wrangle (4.0 L Inline Six) has an intermittant misfire on the #1 cylinder. On the advice of a friend, I replaced the spark pliugs and the ignition coil strip. No change in symptoms. I did notice that if you disconnect the tattery for a short time, the car runs fine for a time, then the check engine light comes on. The light remains steady for a time, and then starts to blink. At that time you can feel the misfire. This seems to depend on the number of times the engine is turned off and restarted rather than the number of miles covered.
My friend seems to think that it could be the ECM, but I have already blown about $150.00 without affecting the problem on his advice, and I would like to get an outside opinion. Any ideas?