Does the charger upgrade kit come with a configured battery tray to replace the enclosed battery box type?

here is no pre-configured battery tray for the upgrade. This part comes with a battery tray and the components needed to update the wiring between the batteries, and the wiring from the batteries to the switch plate. You will need to take the batteries out of the existing battery box and reassemble with the tray. The assembly instructions on this product page shows the steps needed to make the upgrade.