Hi all,
Avan: I am not sure how big or long your scenario was/is but I have once (and once only; at the start of my Sins 'career') come to the point where the whole game came to a grinding halt (that is to say, took me 2 hours for each new planet etc.) in the 'endgame'. I had hundreds of thousands of credits I could not really use (this I hope will change with expansions & mods) and not yet figured out the many horrible things you can do to your enemies to expedite things (although I *was* nuking from afar).
Once you get a good notion of how various elements work, you should be able to progress in most any part of the game, although the endgame lacks some 'extreme measures' atm in my view. I would just start another scenario if you are bogged down...
I started by doing all the prefab scenario's in order, one or two on easy then moderate and now on hard. A fun thing to do is set yourself some 'achievement goals' for each new scenario you try.You will soon realize they are basically 'handicaps' while you play...which means you force yourself to try out many different tactics 8-).
And you can find oodles of interesting tidbits of info (strategy-wise) on these boards if you consult them with some regularity. Or, alternatively, if you manage (unlike me so far) to discover where the mods hid them all
.
Keep in mind the manual does what all manuals do: give you a vague notion of the basics; a few things to get started and keep in mind maybe...and then abruptly end just when you got interested 
Best of luck,
Lucas aka Sinful
* Small have continual plodders ever won,
* Save base authority from others' books.
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* Love's Labour's Lost (WS)