I hunted for a couple of weeks for the gremlin that was preventing my new motor and turbo rebuild for the problem. I finally found the problem.
If you have one of these systems and ever run into dead cylinders, rough idle and other glitches.
Check out the small wire connectors, there are a couple of them. It is possible since they are so small that the miniture male and female metal connectors are not meshing properly. It is possible to plug the two or three wire connectors and one of the male parts will slide by the female part and not make contact. The male part goes along the plastic preventing a connection.