Before you start working on the tone holes, please take the time to check your pad heights.
Other than the holes you cover with your own fingers, the pitches of all notes can be affected by their associated pad heights - which of course have a different effect on the different twelfths that they influence in their position on the tube with the opening of the register key.
It doesn't just affect stuffiness and tone quality, but pitch as well.
With that caveat, have yourself a field day and keep us informed.