You did not mention that it is under warranty. That means that the other components are still quite new. I only suggested a new furnace assuming your was already spent. In my home I have 2 separate furnaces. (single home, not 2 apartments)They control separate areas. I replaced one about 10 years ago. It is a Carrier model. Other furnace is about 35 years old and functions just fine. I have replaced small components on it in the past. I would not replace a heat exchanger in that dinosaur.
You read my post as I explained the burnoff. Seal off the basement area, like you said you can, and none of the initial fumes will enter basement. Then after all is running, vent your home living area, by opening the windows upstairs for what ever duration you think necessary.
SINCERELY WISHING YOU BEST....

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I very much appreciate all the information you gave me. You did the best you could do with the information I provided. I tried notvto be to lengthy so a lot of detail was left out. They are coming this Thursday as the high up here in Fort Wayne is going to be a 57....so I’ll shut them off and crack the small window in with them and will open all my upstairs windows and doors and turn all my ceiling and box fans on and hopefully push anything and everything right out . I will post how we all did after it’s all over. Thank you again for caring enough to respond to my “cry for HELP”.