I had the same problem on my 95 E300 D. First change the air filter, mine was black with crud. While it's out I sprayed a mixture of bleach and water down the air intakes with the vent and ac on. Make sure the mixture flows out the bottom of the cars and the drains are not plugged up. Rinse well. Put in the new filter. I took a week untill the bleach smell went away, but it was better than the mold/stale smell.

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Karl B
95 E300 D
2006 Mazdaspeed 6
2001 GMC Yukon XL
1997 Contour SVT
Mazda RX-7 SCCA race car