Call them up and insist on a recheck, they should not have done it unless left over night. I have the Yamaha 1700 RoadStar, no valve noise just lower end knock on take off or when hot and idling for long periods, all of which are labled as normal.
Try www.yamahamotorcycleforum.com Hop on the 1100 section and compare notes.
I have a Suzuki with loud valve action, WHich is normal for it, VL800 correctly set it sounds like an angry industrial sewing machine. Louder exhaust was the fix for it. I would suggest buying a repair manual and talking with the other 1100 riders and doing it yourself. U will not have any questions that someone(you) pulled a short cut on your ride