I found Stinnett's book to be a mess. He confuses terms & therefore draws the wrong concusions. For instance, one tool that intelligence uses is "Traffic Analysis". This is NOT the same thing as reading the actual decrypted message. Stinnett confuses the reader into thinking this is the same thing. It is not. Traffic analysis is simply recognizing patterns of communications between bases & fleet units. You can guess an awful lot by just knowing who is talking to who, how much & maybe having a cross-bearing on the mobile units, without ever knowing what is being said.
It should also be noted that the IJN code was not actually cracked until AFTER Pearl. We were reading their diplomatic code thanks to some Black Bag jobs funded by Naval Intelligence prior to the war.
It has been a few years since I read the book and do not recall the faults that you refer to. As one of several lines of evidence, Stinnett contended that the Japanese naval code was broken and read by the US in the Philippines before the attack on Pearl. If true, it would force a major revision of our understanding of what we knew of Japanese war plans before Pearl Harbor.
What a crock! I find your criticisms of Stinnett to be total nonsense. Unless, of course, you care to quote some examples. ;-)