1998 CRV - just had new rotors,calipers,pads, drums, shoe's and hardware installed and brake system flushed.?

There seems to be more pedal travelnow than before the brake job. Also there is a knocking or tapping noise that hppens when applying the brakes. This noise speeds up or slows down with the speed of the vehicle. The shop can not find the cause of this and says the pedal travel is normal for these vehicles. Any idea's.