I thought about the ceiling too but it is probably the cleanest part of the interior.
Having replaced the capets and scrubbed the seats, all that is really left is the A/C. I recall spraying an air freshener in the vents last summer, as well as some Clorox disinfectant spray, and that either helped or masked the smell for a while.
An ionizer might be a final solution. Sharper image has some small ones for cars, but I question how effective they are. One of their larger units, like the Ionic Breeze Quadra, plugged in overnight would definitely work.