I recommend that after you finish assembling the bike you take it to a trusted LBS and pay them to tune it up (also recommended by Bikes Direct)... the fact that you could not identify the rubber shim and cable noodle (not know the name but actually figure out what it is for) does not fill me with confidence that the bike will be safe to ride when you are done assembling it.
Congrats on the new bike! Ride it like you stole it!