Dan....
You used the cam alignment tool, right?
Looks like this:

Like Matt said, check the coilpack. If it has even the slightest hairline cracks in it, it will misfire like a son-of-a-bitch. swap out the coilpack with your extra pack, and clean the old one off real good with brake cleaner and paper towels. You will see the cracks, if they are there. High heat epoxy from Home Depot, or Advance Auto will fix it... just make sure to cover the cracks with a healthy coating of epoxy after the CP is completely dry. Be sure to cover the seems, around the base of the terminal boots as well.

I used a 2 part epoxy gel that was rated as high for heat, but it did not run all over the place like traditional epoxy that I have used before. I just recently repaired 2 coilpacks with good results, and had a repaired CP in my mkIII for 30K miles, before it was rearended.
Some of the pictures did not open here, and this is the worst case of a bad coilpack that was repaired I have seen, but you get the idea:
http://www.rocketcat.info/blog/2006/05/howto-vr6-coilpack-repair-step-by-step.htmlApparently dude had no problem after everything went back together.
Same thing, as far as cracking, goes for the cam position sensor. If it is cracked, it is bad, and I have not heard of epoxy fixing that fucker.
I will say this. My brother did his head gasket, and noticed afterwards the car did not run as strong. no misfire, but something was off.... Turned out, the cam position sensor had a small crack in it.
Good luck man!
PS - another cool idea :
http://forums.vwvortex.com/showthread.php?4223032-Ford-Coil-Pack-on-VR6-with-Pics.&p=54863118&viewfull=1