My possibilities have been checked or aren't consistent with your problem. Try pouring and spraying some odor-cide type stuff down the vent and returns and spray from the other end. Maybe something is stuck to the to the vent walls such as grease from the stove. I remember hearing of kids putting limburger cheese in car heating ducts when other guys would hit on their girlfriends. When I worked in the oilfields, we'd have a bottle of the stuff added to gas to give it oder, pour some on a rag, then put it under the seat or dash of someone's pickup. P U!!!!
Post back with the brand, efficiency, and type of furnace you put in and the same info with what you replaced. I'm thinking combustion air, combustion chamber, furnace vent, return or vent, or a plumbing vent.
Could be a dead mouse, rat, squirrel, bird, bugs, etc. in the attic or around the furnace or in the wall or under the floor, under,inside, or behind a cabinet, under or inside the stove, refrig, dishwasher, etc. The nearby movement of air may pull in the smell. Could have a dead mouse in the vent and it stuck to it and didn't get brushed out of the vents unless your son removed them and checked them out. You never know what the cat will drag in. This is what Regina will have to look forward to if she doesn't get the squirrels out of her attic.