New spark plugs turn black after going twenty miles

I have a 1995 triumph sprint. It has just over 6000 miles on it. I put new spark plugs in it and then ride it about twenty or thirty miles and then it starts running realy rough . the place it runs rough is below 2000 rpm. I can get on the freeway and run 90 miles per hour and no problem. I get off the freeway and into stop and go traffic and every time I hit the throttle below 2000 rpm it splutters and then smooths out when you get above 2000 rpm. when I take the plugs out after only a few miles of this behavior they are black again. I have recently cleaned the carbs and synchronized them. The machine is running an aftermarket exauhst three into two configuration. This was installed before I purchased the machine not sure if jets have been changed.