seems silly but how are your spark plugs? I recently had a misfire (although not everywhere like yours) and new plugs completely solved it. I have no idea why - the old plugs didn't show any unusual wear or coloration from rich/lean running, but it did, and I'm glad!

back to misfiring...I've always worked backwards to trace the problem - first plugs, then coilpacks, then air leaks. Three things can cause misfires - not enough spark, loss of intake charge boost/overfueling as a result, or spark is ok but air/fuel is boosted to the point where it blows out the spark.