Death Comes to Time, Scream of the Shalka and NuWho can't all "really" happen together in the same continuum though, if you catch my drift.
But now you're talking about something else entirely.
Canon refers to something that is authoritative, official, and sanctioned. Insofar as the BBC is concerned, all three stories bear the official BBC mark. Canonicity is presumed in absence of other evidence, and the BBC has never said that
Death Comes to Time or
Shalka are not canon. (Now, Paul Cornell has said that, in his opinion,
Shalka is no longer canon. But, frankly, he's not in a position to make that determination.)
You're talking about
continuity. Which pieces hang
together. And of the three I cited and you've repeated, the only one that
doesn't hang together with the rest is
Death Comes to Time. I can fit it into continuity (it's an archetypal story about an archetypal Doctor and an archetypal companion, but the only way that we non-archetypes can understand it is if it uses characters in whom we have a connection), but that's a purely personal decision. There's no reason that
Shalka doesn't fit into continuity; it's just a question of where Richard E. Grant goes in the Doctor's timeline. (I see no reason that he can't go in between McGann and Eccleston, frankly, in spite of dialogue in "The Lodger.")
Ultimately, canon is an objective descriptor (whether or not it's official), while continuity is more personal and, thus, more subjective.