Re: Big B Bari intonation
To surmise a guess, I'd need to know how your relative intonation was octave to octave (do C1, C2, C3 sound in tune with each other, for example). Once that is nailed, then I'd need to know what specific notes were flat or sharp by how much.
Knowing nothing else, if C# is flat but everything else is ok, then I'd say your upper stack is set up a little low. Regarding relative intonation, how does C#1, 2, and 3 sound?