Unfortunately, the manual isn't all that specific with actual game mechanisms. There are a number of helpful threads here at the ORG (see Tea House -> Confucian Academy) as well as over at TWCenter which attempt to uncover things through meticulous testing and observation. Trade, economics and diplomacy are some of the harder nuts to crack. Modding the game also can be informative as you can observe what happens when changing key variables. So a lot of the more specific information is littered about, unfortunately, and still open to speculation.
Frogbeastegg's guide is likely the most comprehensive resource and Darkside's Economy guide for S2 (at CA's forums) also has some good information. What we really need though is someone from CA to come by and do a Q&A regarding some of the more mysterious game mechanics. A nice fellow called Thamis (Jan van der Crabben) used to drop by at TWCenter back when Empire was released an posted quite a bit of the finer points of how the economic systems worked. He was the developer responsible for much of the economic systems inherited by Shogun, I believe, but has since departed.
Making certain you've moused over absolutely every last bit of text and icon elements in the UI is also surprisingly informative. There are a number of useful things hidden away there as well as some misleading information on game mechanics. For example, one tooltip for public order implies that happiness (vs repression) has a positive effect on growth. Unless there is some hidden bonus, this appears to be an abandoned concept. Instead, disorder leads to negative growth and happiness and repression are effectively equal (at least as far as the economy goes).
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