AND, sir, let me say that I would be proud to share a cockpit with you any day. Cheers!
Thanks a lot AirRabbit, that would be an honour, sir. I think this has been a well teased out debate.
The preceding airplane did not change, except for the possibility of flap retraction (if the JAL crew delayed that long) – which, as I know you recognize, would only decrease the severity of any vortex generated
I glanced over some of the evidence at the public hearing tonight - unfortunately not enough time to delve too deeply - but did find some of the relevant parts. As far as flap retraction making a difference is concerned, until being reminded, I would have agreed with you on that point - but it seems we would both be a bit wrong, at least according to Dr. Proctor(chief author of the wake vortex report for the NTSB), who stated that he thought flap retraction would have very little effect on the strength of the wake vortex. In his opinion, the main factors were weight, speed and wing span. He also stated that even the initiation of climb, with the accompanying change in wing loading, would have very little effect on the strength of vortex generated. Personally, I fell compelled to apply a little scepticism to some of his opinions, in light of the fact that when asked what effect the presence of winglets would have on the strength of wake vortex - he stated that he could not answer?!? It has always seemed strange to me that the chief author of the wake vortex report refused to answer some of the questions concerning the relevant matter and cited the reason for doing so by saying he was not an aerodynamicist.
Another matter which was evident in the wake vortex report was a discrepancy between the 'ambient' winds which both aircraft flew through and were recorded by their respective FDR's. Considering their closeness in time and space, Dr. Proctor only acknowledged the difference, but could offer no possible explanation for it. Maybe the presence of at least some turbulence? Maybe - maybe not
With the amount of experience humans have in discerning a one-hundreth or a two-hundreth of a “G” difference, I would say that anyone would have concluded that these two encounters were, at the most, very, very similar.
That brings me to you point about whether of not the PF thought the second encounter was “more” than the first. The FDR seems to refute that idea.
Dr. Proctor stated during questioning that he believed that it was possible the accident airplane could pass through the core of a wake vortex and leave no indication of the passage on the FDR. That puts us in a paradoxical situation! Considering he was the official "wake vortex man" - If I accept that statement in isolation - it strengthens my argument and weakens yours - If I reject it, it weakens my argument and strengthens yours?!? 
But he also stated that he thought the wake vortex counter would have been "nothing extraordinary". That leads the two of us back to our discussion about the efficacy of the FDR's acquisition rate. But I'm just getting to one of the points which threw doubt up for me early on. The paper titled ""An Engineering Study of the Unsteady Response of a Jet Transport During a Wake Encounter and the Transitional State of Potential Crow Instability", and the work/remarks of Dr. Anthony Brown, NCA Canada. Dr. Brown has an interesting, indeed probably valid, explanation for events that day and how the FDR, pilot perception and APC could have played out - that is if we accept that these conditions existed on that day - Howevr, Dr. Proctor dismissed the idea completely.
My point isn't that I accept or believe the suggestions of Dr. Brown - but rather it's something which makes me approach the conflict of ideas with an open mind - as opposed to just accepting Dr. Proctors evidence, who, IMO, demonstrated quite definitive opinions sometimes - but refused to give answers at other times - which I think should have been within his area of expertise, if authoring a report on wake vortices. At the end of the day, I find it difficult to even form an opinion on who is right - I'm not an expert in that field, Dr. Proctor was called to report/give evidence and Dr. Brown wasn't.
I think the PF was nervous about the JAL B747 – probably more nervous than the Captain or you or I would recognize. I think the first wake encounter (handled nicely by the PF) merely made him more “on edge” in anticipation. With the on-set of the second encounter, I think the PF’s self-control was severely taxed, and he over-responded physically while trying to sound like he had everything under control.
It seems like your suggesting that PF was primed to expect a wake encounter. I think that was discussed at one point during the public hearings and I tend to agree with you. It's probably something which I've tended to overlook a bit. The first time I ever read the CVR transcript - I thought it a bit strange that he should ask that, considering his experience level.
I hope all of us in the industry have learned from this accident and all the discussions that have taken place as a result.
Hopefully! Concerning what "design manoeuvring speed" means, I think it has woken up a lot of people, and maybe refocused attention on the importance of a few related things such as turbulent air penetration speeds, etc.
While I feel quite strongly about my reservations in this case - in general I think the NTSB do an outstanding job, and not only within the US - many states around the world call on their expertise or technical assistance. In certain circumstances it sometimes looks like they have to step into a bear pit of parties and their conflicting interests. To me, it always seems like they lost their naivety over the 737 rudder reversals issue. The only room for improvement that I can see is with the relationship between the NTSB and FAA over the timely enforcement of NTSB recommendations. Since many places around the world take their lead in regulatory matters from the FAA, it's a matter that concerns safety both outside as well as within the US.
Maybe we'll meet up here for another debate on some other thread at some stage, and I'll look forward to that. 
Regards.