Netviper, if you are still having trouble, try a bleach solution. If you can, remove carpet and soak for a few hours. Then, wipe the inside of the trunk, let soak for 5 minutes, then wipe off with a clean wet towel. Do not use concentrate beacuse concentrated bleach on bare aluminum is corrosive. Last step, totally expose the inside of the trunk to dry in the sun and let the carpet dry in the sun for atleast a day or so. The carpet must be totally sunned to remove all moisture which breeds the bacterior. Read bleach directions and wear gloves.
P.S covering up smells does not always work; you must kill it at the source.