Darktable Negadoctor: I must be holding it wrong. Any advice?

When scanning the film you should try to get as much light onto the sensor without clipping the highlights – so you have maximum dynamic range without any extra noise coming from boosting the exposure later – thats the only user error imo.
The film looking a bit cooked is probably not on you – you said you took the photo mid 2010, but when was it developed, how was it stored? The yellow color of the negative is unusual.
And as for the negadoctor steps… It is a lot of clicking back and forth, the manual talks about everything but looking at it now the process itself isnt really described there, right?