THanks for the info. I did do those things. I also checked the input side of the coil, which all 3 coils show as a constant 12v. I took the plug wire off a good firing cylinder (1) and checked it for spark (good) then did the same for 5 using the same good wire (no spark). i will change the boots on all the coils even though i think I have proven them OK by substituting one for another.
A question. Since I was having a sporadic missing problem and decided to change the plugs, it was due, then uncovered the bad harness issue, IS it possible that --- 1. THe harness could have damaged something. 2. The system is smart enough to shut down the cylinders associated with the number one coil, assuming that it was the one missing at the start and need to do something to allow it to work again. Also in my testing of the old harness, after removing it I traced the structure of the wires to each coil and they seem to be made up off 2 wires into each coil, 1 is a common which comes from a wire terminal block on the left wheel well, Is this the ground? and the other is a seperate wire for each coil originating in the large multiwire terminal connector. I assume this is the pulse side for firing order.