The Beetle body parts crate can be found at the base of a gorge near the Silver Casino in Silver Canyon.
Nearing the part will trigger a sonar beep, and will increase in rate as the player nears the part. Collecting the part, once prompted, will deliver it to Rav's garage on Airfield 73.
The player is required to complete the Mac: Shift-Lock questline in chapter 3 - City Lights and collect the Beetle chassis, before they can collect the body parts crate.
Collecting the body parts crate will deliver it to Rav's garage on Airfield 73.