I have a similar problem on mine that developed after little welding got done to it, so if you did any with your new muffler going in and all that it may be related to your electronics. Otherwise the sky is the limit, trouble shooting of intermittent problems is a bit tricky. If you think it is related to your ECM check out my post which is just next to yours on Trooper ECMs.

Good judgement comes from a lot of experience and a lot of that comes from Bad judgement

3.4L 91' Trooper
4.3 TBI, Airmax 1" TB spacer