A bit of stink owing to dust burnoff is normal for any system. We need to see the wiring diagram off the new motor. And so now I present. Proper ductwork design and installation is a major undertaking. The system might not operate at peak efficiency, but it will work. That said, if excessive dust is accumulating on aux strip elements, then it is also accumulating on refrigerant coil
That for sure would cause the classic XJ heat not blowing problem.
Dust buildup on auxiliary heat coils
I only need the high speed setting as the air handler is older and not setup for multiple speeds even though the old motor was multispeed. People are now beginning to look at this type of heating more seriously. If the fan stays on it is in the air handler. If the level is too low for too long, the compressor might overheat and fail. When they crack, the CO leaks out.