Hello Will,
To answer your questions...
1. Yes please use foam/ insulation materials behind the TMP006 PCB in order to reduce the effect of air through duct acting as a noise source. This will allow the TMP006 mocal temperature to be stable.
2. It all depends upon the kind of accuracies that you intend to achieve. You will not obtain more than 2degC accuracy for such large target distance applications. Can you collect the data after insulating the device and see if your issue is resolved?
Regards,
Abhi