"How long were you doing this project?" is correct, because you are measuring time for a short-term project. We sometimes say, "How long did you do that job" when talking about someone's old job, but that's usually something measured in years, and we really don't use that kind of phrase for other topics.

It depends whether the person is still working on the project or it is fully terminated ! If he/she started the project earlier in the past ( near or far) ,yet it is not finished yet , you would be asking : " How long have you been working on ( doing ) this project ?" The present perfect continuous tense here refers to the project having started in the past and still going on in the present . Whereas if the project is terminated you 'd rather say : " How long did you work on ( I sounds more suitable than using the verb to do here) this project ? " The past tense here indicates that the action is finished in the past and the project is terminated and you are inquiring about the time spent already working on it in the past !

What about "How long have you been doing this project?" As a man above me said, you are measuring time for that project but you have already started in an unspecified point of time. That's why I am suggesting present perfect continuous.