I'm chasing an intermittent misfire on my V6 which was occurring only under load but is now occurring a bit at idle as well. Its a single coil pack with three coils mounted above the front bank of plugs, but also connects to the rear bank through plug leads with each coil firing two spark plugs at once.
As you say there's no way to swap them around, also testing the spark from the bottom outputs that go directly to the front plugs is difficult. The way I did it was to lift the whole coil pack out leaving the insulator boots in the spark plug towers, then make some extension leads to go from the coil pack to the boots, I was then able to disconnect individual plugs to test the strength of each spark, also you can do a cylinder drop test to see which cylinder is misfiring, although by the sounds of it you already know which one it is.