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The pleated filter normally really should not create enough resistance to cause blower motor to over heat enough to cause a burning smell.
What is model on the furnace itself?And do you know if it has an ecm variable speed motor?
Gas or electric heat?
If electric do you have the RE or EB series? And how many KW heat ?
I suspect this may be a motor winding issue.Can you swap the fan speed wires to different terminals to see if the smell goes away.(Example, move the heat speed wire over to the fan terminal) and see if you start getting the smell in heat mode and not in fan On mode.
If you can look on furnace and get me a model I can try to pull a manual and show you how to do this.