I think you're just going to have to keep cleaning it again & again, and again! Some great suggestions above though. The Valetpro enzyme eaters work very well - suggest you try these on the upholstery.
My ED30 had the smells of a smoker - it has no ashtray, so presume they only ever smoked windows down.
The whole car was wet vacced when I bought it - I've had the aircon cleaned and refreshed a couple of times, every surface has been deep cleaned, & the windows cleaned every few months.
There's no smell now, but I am still surprised at the dirt coming off the inside of the windows, even considering how long it has been in my ownership & the no of aircon cleanses. Just shows how long the muck stays around for...