I know that bacteria and mold can grow in the ducts if you don't use them. That is why you get that funky smell from your A/C when you first turn it on after winter. You might try spraying Lysol down the vents and see if that helps kill whatever it is you are smelling
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Where did you have it parked when it sat. Rats and mice love blower motors since they use a wheel style fan. Dones it smell dead, it isn't that unusual for them to get stuck in there.