I don't know about the pollen filter, but the bas smeel usually comes from fungi growing in the system. The best way to get rid of this is to take the car to the nearest decent car wash have them pump Ozone through the vents. This kills off anything that could cause a stink.
I don't know about OZONE, but pop along to your local AC man. And he or she should be able to supply you with antibacterial spray to kill the fungi that cause the smell.
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