It's frustrating that the engine is clearly misfiring and yet no codes are stored. I'm sure it's like you say where only severe, sustained misfiring is enough to trigger a code.
What I'd like to know is whether or not misfires are logged in the ECU despite not triggering a CEL or storing a code. I'd think this could at least point us in the right direction or maybe narrow down a particular cylinder.
Has anyone ever tried running Techron or some other fuel injector cleaner just to see if it makes a difference?