I finally got into the PTU harness and hardwired the new connectors onto the stock harness. Before this I always had a miss/stumble when cold and would go away as soon as the temp needle moved off the pin. I had cleaned, dielectric greased, rerouted, etc.. the subharness and I assumed the problem layed elsewhere. Now I have no issues whatsoever and the car runs better than it ever has.
I would bet your problems may lie in this connection if you haven't hardwired it yet.