Our 2005 Honda Odyssey runs fine for a few minutes then runs rough for about three seconds. It feels like you’ve just hit a patch of rough road. It does this again and again–few minutes runs fine–few seconds runs rough.
Sounds similar to my problem with the same year van. Thought it was the plugs. Took it into the dealer and discovered it was the engine mounts. Check out the discussion on engine mounts on this site.