Russ, your list of points is valid, even if some could be discussed. For example : how can you be sure that Sovier Union will continue to sell things to Germany and allow transit between Germany and Japan until FFO-Barbarossa begins ? Stalin could close the door perhaps at the end of 1941, feeling strong enough at that moment (after all, Hitler won't attack before spring).

Now, did you ask yourself why Jacques decided to keep Pearl Harbor strictly identical to OTL ?
He could have game it from scratch and we could have seen results ranging from "early detection of Kido Butai and US attack launched" to "same surprise as in OTL, but 3 US CVs were anchored in PH and are sunk".
I think it was necessary to maintain PH "as is" to keep the game under control.
Same thing for the German decision to attack Russia, for example.

We are writing a story here and have to make "editorial" choices (I don't know if it's the right word), which will affect the whole story.

We have ONE main POD (France fights on around 15 June 40) and several smaller PODs (you listed some of them, there are plenty others).

So I agree that the Japanese will benefit from Allied documents found in the PoW, perhaps more that in Singapore OTL, but we can't turn the whole story upside down. This has to be a minor POD. The problem is to keep it under control.