1) To get the best AI you'll need to make or modify a script incorporating Dark AI commands - search for Dark AI on these boards and you'll see some sample scripts to use.
2) Timed missions - yes.
3) There is a tutorial on animated HUDs - search these boards and you will find it.
4) Yes - i think this is even explained in the manual.
Some advice - this forum contains a LOT of useful information, but it make take some time to find exactly what you want. Before posting a question - try searching the forum as you'll probably find someone else has asked the question before.
Good luck with your game.
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