Well.. The fuel trip - if I understand it correctly - relies on a feed from the fuel level sender unit. If I were you I'd trace the wires from that. They're likely to be small and weak because they're only carrying a piffling signal current, so if the people at the bodyshop tweaked them lightly, they may have severed the connection.
Did they have the carpets out etc?
Look for the fuel sender unit's wires (under the rear seat squabs I'd guess) and follow them looking for signs of strain on the sheathing. Find the connectors where they join into the loom, and see if they're connected properly. There are probably two wires: one for the computer and one for the gauge.
If that doesn't get you any closer to sorting it, use a multimeter to check that you're getting continuity though the wires, and then check to see if you're getting a voltage from it.
Another simple thing would be to go to the body shop and ask them which wires they disconnected: point out the problem - maybe they can shed light on it?