Help this newbie; the docs for this game are vague

[gregdabuckeye]

Please help me with these questions about this game. I am currently running the demo and want to get the game if I can resolve these problems.
How do population and happiness affect production? I seems a planet with a few people crank out just as much production as a populous one. Happiness and reproduction bonuses seem worthless. What does the tolerance modifier do?
How does intel work? It doesn't seem to be allocated like research and let me know how my projects are doing.
How do support pods work?
The 1500 racial advantages (e.g. temporal and psychic) seem of marginal value. Does their special tech tree ever seem to do anything but give you cool text about your weapons that seem just as good as standard ones?
Waypoints with cargo ships seems a pain because your ships end up dumping cargo at the waypoint and continuing on. Am I doing this wrong?