OK, left to go for lunch at the oldies, took all of 5 minutes and the miss/stutter started, about 13.8v on the gauge, so unless the gauge is off it does not look that the alternator is overcharging. I pulled the light switch and the miss/stutter stop! Turned the lights off and drove for about 5 minutes and the miss/stutter came back again, pulled the light switch and stopped again.
When I left the oldies (lunch was great as always) I did not have one single miss/stutter, but seeing it was raining I had the wipers going (not sure if that is part of the temp fix). And seeing that I am sort of getting a grip on this gremlins behaviour, I go as far to say that when the miss/stutter is there it feels like the whole Heep runs diff, shifts somewhat less snappy and also think it seems less powerful, fix it with the lights on off trick, and it feels like the Heep gets put into sports/extra power mode.
I also had a good look and my Heep has an aftermarket wiring headlight loom installed, it has 2 relays (I think thats what they are) and maybe the problem is coming from there somehow, I am willing to have a go at making and installing this
http://jeep-xj.info/HowtoHeadlightLoom.htm or even remove this after market headlight loom to see what happens when I drive without it.
My understanding of electrics is just not good enough for me to say yeah the problems is due to this or that, even seeing the headlight on off trick seems to indicate something being wrong in the wiring there, I first thought it might be the alternator as it could be overcharging, but the voltage gauge is not really going past 14v.
PLease feel free to add or throw an idea on to how to test or look at something else, I am waiting for that OBD2 plug in scan thing to come in before I go and try something else, as I hope that thing might show something.