On many cars,the yellow on the bumpers is actually the color of the bumper.As for your scrathes,if they are as deep as you say,I would recommend taking the car back to the dealer for the "FREE" repairs.If you were to do it yourself,you would have to buy some touch-up paint,towels,etc.If he wasnt a shotty dealer,then they will do a good job.After all,the sales guy isnt the one doing the repairs,right?
If you do take your car back(Which I recommend) it will be in good hands.It will be repaired by people that know what they're doing.(I hope).And since they are repairing it,they should get these "Speckles" you keep talking about.Bottom line,if its from the dealer,and its free,take it.