you can negotiate that into your settlement, but they want all they can get and they charge a bit to let you keep stuff.
You see, they sell the bike and if the pipe and stuff is missing they are selling a parts bike missing parts, not worth as much.
Best is ti take your settlement and let them have the stuff, or find out what salvage yard got it and buy the parts from them.
Now having said that, you are allowed to get personal stuff off the bike as long as you keep the bike whole, so retrieving a power commander or something like that is possible if the guys at the salvage yard are not real attentive.