Gave this a read too - there were parts I enjoyed, and parts I didn't. A few plotholes I felt that should have been tidied up - most notably the signal coming from the military base which was dropped like the proverbial hot potato and never followed up on. Never explained why or how Davis had the file on Otto in the safe or had information about his visit to Saigon - (and even if he were to have the file for security, why he would have kept it in the safe on a military base beggars belief) - nor what his stake in the situation was. Likewise, the fact that MI5 had already connected the theft of the documents to Davis and the military base and had, for whatever reason, not revealed that information to MI6 (who couldn't theoretically act on UK soil anyway) makes them culpable in the ensuing chaos, perhaps even more so than MI6 - yet this isn't even mentioned, by Bond (or Mallory, who must've known about it).
If I was Bond, I would be pissed off that the sister service had been keeping secrets about having a lead on the theft than anyone seems to be during the investigation.
M released Silva to the Soviets in 1962 - but Bond doesn't appear to know whom he was. If he was as important as Silva seems to be - and, indeed, as M suggests he was - then it's surprising that Bond wouldn't have been aware of the sacrifice, or at least, of the swap of agents given that by 1962 he was a seasoned Double-Oh agent. I'm also a bit puzzled about why the UK would have a top secret file on US troop deployments - surely that says more about their inability to keep documents secure than the abilities of MI6.
A similar puzzle is how Mallory knew that Bond was taking M to Skyfall in enough time to get Andress there shortly after Bond arrived. Or, indeed - how she got there as later there only appears to be the Bentley outside and no other car/motorbike and she presumably left a long time after Bond - unless we are to believe that Bond told Mallory he was taking M to Skyfall. And the dialogue between M and Andress about 'taking care of Bond' didn't quite make sense - this is the first time the two must have met, outside of the enquiry, given that she's not even his (or even, really, Mallorys) subordinate.
That said, I appreciate the time and skill it took to put the project together - I know how hard it can be to put something like this on the page. And it was, even with all my quibbles, an enjoyable read. But curiously, the parts I enjoyed more were the parts that diverted from the established plot and script and went into uncharted territory whilst keeping the same concept (thus the pretitles sequence and the sequence at the military base).