cnuttgirl,
What year is your Exby? I have seen posts that show the A/C filter unserted into the rear of the blower housing on the front passenger side of the Exby (right above the feet of your passenger - better make sure your passenger has clean smelling feet!!!). Unfortunately, I have heard they are discontinued, at least for my '98, and that the last couple of filter kits were purchased off of Ebay not too long ago.
I have not heard of a filter for the rear unit, but if you think about it, fresh air is not brought into the truck back there, so a filter would not be as effective.
Finally, the smell would be a mold or mildew growth, and I think a filter would not help too much with that.
Check your condensate drain tubes, and make sure they are clear and not holding water back into the evaporator housing, as this will cause nasty stuff to grow in there.
Finally, Ford has a solution to spray into there. I would think that something that kills mold/mildew, like ammonia, would be better than lysol which disinfects and does not touch the mold/mildew.
Hope this helps.