I thought the exact same things, but I'd argue that Japan was largely successful in their objectives. Admiral Yamamoto knew the enemy's economic strength and military potential and told such information to Japan's war leaders/planners. He even told them he could only deliver a brief period of victory (1-2 years) before the weight of the enemy became too much for Japan to take. They were able to accomplish all of their objectives until Midway, which is arguably the last building block in Japan's desired defensive perimeter.

The author also seems to make the argument that Japan was in a total-war situation with America and its goal was to get America on the ropes and capitulate. That would be crazy if it was what they thought. The Japanese goal was to push the US (and other Western powers) out of the region then build a defensive perimeter to make retaking the region so costly in lives and treasure that US public opinion forces US leaders to make peace.

I've always felt that the miscalculation on the Japanese part was more along the lines of predicting American resolve and the pace of technological change. Japan's leaders didn't expect the "total war" mentality to take over as much as it did (i.e., total victory at any cost, unconditional surrender or the war continues) and breaking Japan's naval code was a huge blow to Japanese planning. Once all that happened, there was no way Japan or anyone else could win that war against the US. And the US was able to use it as a springboard to superpower status and eventually become a hegemony.