Rick - did you have to solder in new injector clips in or did you reuse the 19's and left the injector harness alone?
The reason I ask is because in the last 3L I did, I soldered in the 3L's clips onto the CSVT's harness and had random misfires in one cylinder. I later deduced it was a bad wire in one of the injector clips and swapped out the culprit and vio la, no more misfire. For me it was easy as it would misfire consistantly, and long enough for me to pull the spark plugs and find the one that was carbonless (due to lack of fuel).
At first I thought it was an ignition issue as well and after trying my new Magnecores out of the box on the car it still did the same thing.
Now...in your case you say it clears up...but dsoes it clear up for good during the time following the misfire or does it return while driving at all?