I have to ask a couple of questions before I can get an idea for what's happening here.
Does is cough and sputter is 2nd gear if you take it above 2000 r's?
Basically, does it ever happen at lower mph with higher rpm's?
In the higher gears (ie. 4th) you will be maintaining a more constant engine speed at the precise rpm that may trigger a problem in your ignition to manifest. In the other gears, you are crossing the threshold too quickly and don't notice the "miss".
If this was a fuel starvation problem, it should happen in any gear when the rpm is high. Try and make this problem occur in second gear around 2000 rpm. I've had several problems like this and most could be traced back to the ignition.
84 CJ-7/258,Weber 38,Jacob's Omni Mag,flowmaster,3.5" SL,32" BFGMT, Superior 1 piece