I wonder if by the original furnace overheating it sent enough hot metallic smell/substance into the duct and that is what you're smelling.
Rex, this may be the correct answer. Almost like cigarette smoke that clings to things, I think the same thing happened with this odor. It would smell worse when the ducts were heated longer, much like our used car that may have been smoked in, even after it's been cleaned and years later, when it gets hot it sometimes emits a "smoky smell."
Anyway, we replaced the 3 silver ducts with an insulated duct. The insulated duct is much harder to work with in the limited space, but we made it work.
Testing initially smelled the same, but also had a "new ductwork" smell. So we ran it for a good while, and the smell got better and better, as opposed to worse!
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