1st off- display reductions are usually at the managers' discretion, so unless there was a dent of scratch you'd be lucky (or unless they screwed you for the other components).
2nd- Absolutely. Ask for details of everything, you would also need the individual instruction books, all accessories that came with the components, even the packaging. You paid for it, you deserve the spare leads! I once had some local-yokels try to pass off a 3GB HDD as 30GB, you should check the spec for the entire system (including all fans, coolers etc.) against the itemised bill.
3rd- You can probably let this one slide. For a silent PC, the Raptor will probably be louder than even a cheap HDD unless they're suspending them for you.
Finally- "How to make certain a system is correctly built?" Simple. Genius, really.
Have them demo it for you, in a quiet room.
If you can hear it, take off 5% for every excuse they give. Pretty soon they'll want more time to "finish it off for you"