"Time out while booting. You will have to manually upgrade the board using the uploader plugin"

Most CC3D boards still use the old bootloader (v3), you may need to update it to the bootloader v4 and got working the automatic reboot needed for Vehicle Wizard.

See how to update the bootloader here: Firmware Tab

If the firmware upgrade step fails during the wizard you should update the firmware manually before proceeding with the wizard. Please find the alternative firmware upgrade method here: Firmware Rescue.