I will attrmpt to explain the problem then the troubleshooting steps we have attempted. Need other minds to find solution.
Have 87 Trooper II that we purchased an engine from EverDrive to replace blown engine. Engine passed EverDrive's tests. When engine was installed had new plugs, rotor and distributor cap. Carb was not rebuilt. Engine starts and idles rough. Idle mixture plug still in carb so unable to adjust mixture. Timing was set-no change. Removed Number 1 cylinder plug wire no change in rpm. Reinstalled wire, remove cylinder 2 plug wire-no change in rpm. Reinstalled wire, removed 3 and 4 and these wires had drastic rpm change. Removed 1 and 2 plugs and they were sooty. 3 and 4 showed normal firing color. Changed wires between 1 and 4 and 1 still had no rpm change when removed. Performed compression test and all cylinders were between 128-130 lbs. Increasing engine speed gives the impression that engine smoorhs out but removing 1 and then 2 still makes no rpm change. Not 100% sure that all vacuum lines are in the correct locations as diagram is hard to read and EverDrive had removed some of the lines.
Any theories will be tried.

FIXED-Tried replacing coil and rebuilding carb. Problem still existed. Removed every vacuum line I could find and started replacing them, also checking each vacuum switch, checkvalve or electric vacuum swith. Compared the EGR vacuum switch with one from bad engine. The one that wasn't running right held a vacuum when applied. The one from the engine that we replaced had a vacuum bleed off. Exchanged the switch and the engine started running right. Not sure if there was an incorrect routed vacuum line, or the switch was bad. Either way problem solved.