Have you tried taking the seats out for a more thorough cleaning?
At last resort you can have the seats reupholstered.

A cat carrier with a solid bottom is a good thing to have.  
I have a "Pet Taxi", which has a molded plastic top and
bottom with a wire door.  It comes apart for washing.

I once had a neighborhood tom cat spray in my car when I forgot to roll the
windows up one night. Phewww. Here's what I did, and it worked. Get some
"enzyme" cleaner, specifically for pet odor. Nature's Miracle is the one I
used, but there are others on the market. Spray it liberally on the spot, keep
it moist for at least eight hours so it can work. (A Bissell Little Green or
other portable "steam cleaner" is great for this) Don't use any kind of
detergent before using the Nature's Miracle. Then I took my HEPA air filter out
into the car, and let it run. Re-apply the Nature's Miracle if itt doesn't work
the first time or two. Good luck!!

Sherry

I take it that you have not succumd to the vicious persistent clamor
of those who would shove you towards sexual mutilation upon your male
cat. This is very good. We could never visit such a barbaric
monstroisity upon out little guy either. It is far better for us to
endure what nature intended rather than change his little life forever
with the totally unnecessary and cruel procedure know as 'neutering'.
Thank God there are some left among us how have transcended our own
self-centeredness.
Thanks, Jamie. It was good to read your post.

IBen