My Tuning Issue Seems to Be A COP issue.
 

After driving the car to class today to see if I could sort out the fuel map, I couldn't get over the fact the car sounded like it was running on 3 cylinders. So I pulled a connector on the front COP and the car started to die. I put it back on and pulled the second. Again the car sounded like it was going to die, and I could hear the coil firing on both one and two. Then I pulled the connector on the third, no change. So I pulled the connector on the 4th COP and again, no change. So I swapped the assumed non working COP's to the front two cylinders and tried again. The results were the same but in the reverse order. Based on this I'm guessing my harness is fine, but maybe I had two COP's die at or around the same time? Does that happen often? And more surprising is that my car can run on just two cylinders.

should be able to feel/hear them working. (use a screwdriver and put your ear to it)

if you have a mspnp2, you can use the output test mode to fire them off without the car running to really narrow it down.

I can hear the two working COP's clearly. The other two aren't making a sound.

what happens when you swap coils around?

having #3 and #4 both not work is odd, not what I'd expect.

I'd expect you to not have 1&4 or 2&3

COPs do die. Fords are known for this. Also, you need to use a different dwell setting for COPs than for OEM coils (look at Brain's COP sticky). If you didn't do this, then early death will result.

If there were a problem with a spark output channel, you'd be correct. Coils are wear items though, and their finite life can be brought to immediate end if not properly configured.

When they die/are in the process of dying, will their problems be exacerbated by bumps/vibrations? I know it sounds silly, but i'm trying to avoid pulling the entire damn car apart to find a wiring issue.

Chasing a misfire on our car right now that seems to happen sometimes over bumps, and this past monday it fired up on what sounded like 2 cylinders. Opened the hood, checked plugs and such, but didn't unplug anything since i was trying to get home. Shut hood, car magically ran fine.

Has never once misfired under boost. Have heard that weird things can happen when these Denso COPs start to get old.

The car runs rough, although drivable until I pull one of the working coils. Even after reconnect the working coil the engine can't recover and dies. If I pull one of the non working coils nothing happens. The sound and RPM stay the same. Like I said I'm a little shocked the car will run on only two cylinders. Not well but it runs and is drivable.

The new coils are in, and the car sounds far better. I'm looking at the COP sticky to make sure my dwell is correct before I start working on tuning.