I had a problem much like this. It would drive fine while cold, and for a short time while warm, but eventually it would get an erratic misfire.
Digging into this probem, I found that water had gotten into the rear three spark plug tubes, with evidence of water on the rear bank coil pack stems, and some slight rust on the exposed metal of the spark plugs, I checked all the coil pack resistances, all in spec. I unhooked the coil packs one by one, and noted that while unhooking one would make it a steady misfire, and pulgging it back in would go back to the erratic misfire, doing so to the #1 coil pack would result in a smooth run for about five seconds after it was plugged back in.
Threw a new set of plugs in, and got a new coil pack. Got it hot to replicate the problem, shut down, put the new coil in #1, and fired 'er back up. It's been fine ever since. Paranoia being what it is, I got another two coil packs, and new gaskets for the rear coil pack cover (backordered, thanks Honda Canada...), which I'll be throwing in this week for total peace of mind.
Any evidence of water in your rear cylinder bank plug wells?